diff --git a/CHANGELOG.md b/CHANGELOG.md
index 039117fb25..0b9c0015b0 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -4,7 +4,7 @@ See the [releases page](https://github.com/github/codeql-action/releases) for th
 
 ## [UNRELEASED]
 
-No user facing changes.
+- Organizations can create a custom repository property named `github-codeql-tools` to set a default CodeQL CLI tools value. You can optionally set `github-codeql-tools-mode` to control scope: use `enforce` (default) to apply to all workflows, or `dynamic` to apply only to dynamic workflows. If a workflow provides an explicit `tools:` input, that input takes precedence. For more information, see [Managing custom properties for repositories in your organization](https://docs.github.com/en/organizations/managing-organization-settings/managing-custom-properties-for-repositories-in-your-organization), [Repository properties for Code Scanning](https://docs.github.com/en/code-security/concepts/code-scanning/repository-properties) and [Customizing your advanced setup for code scanning](https://docs.github.com/en/code-security/code-scanning/creating-an-advanced-setup-for-code-scanning/customizing-your-advanced-setup-for-code-scanning).
 
 ## 4.36.0 - 22 May 2026
 
diff --git a/lib/entry-points.js b/lib/entry-points.js
index 0e7010b990..b000954ff2 100644
--- a/lib/entry-points.js
+++ b/lib/entry-points.js
@@ -150410,11 +150410,14 @@ function getUnknownLanguagesError(languages) {
 }
 
 // src/feature-flags/properties.ts
+var github2 = __toESM(require_github());
 var GITHUB_CODEQL_PROPERTY_PREFIX = "github-codeql-";
 var RepositoryPropertyName = /* @__PURE__ */ ((RepositoryPropertyName2) => {
   RepositoryPropertyName2["DISABLE_OVERLAY"] = "github-codeql-disable-overlay";
   RepositoryPropertyName2["EXTRA_QUERIES"] = "github-codeql-extra-queries";
   RepositoryPropertyName2["FILE_COVERAGE_ON_PRS"] = "github-codeql-file-coverage-on-prs";
+  RepositoryPropertyName2["TOOLS"] = "github-codeql-tools";
+  RepositoryPropertyName2["TOOLS_MODE"] = "github-codeql-tools-mode";
   return RepositoryPropertyName2;
 })(RepositoryPropertyName || {});
 function isString2(value) {
@@ -150432,7 +150435,12 @@ var booleanProperty = {
 var repositoryPropertyParsers = {
   ["github-codeql-disable-overlay" /* DISABLE_OVERLAY */]: booleanProperty,
   ["github-codeql-extra-queries" /* EXTRA_QUERIES */]: stringProperty,
-  ["github-codeql-file-coverage-on-prs" /* FILE_COVERAGE_ON_PRS */]: booleanProperty
+  ["github-codeql-file-coverage-on-prs" /* FILE_COVERAGE_ON_PRS */]: booleanProperty,
+  ["github-codeql-tools" /* TOOLS */]: stringProperty,
+  ["github-codeql-tools-mode" /* TOOLS_MODE */]: {
+    validate: isString2,
+    parse: parseToolsModeRepositoryProperty
+  }
 };
 async function loadPropertiesFromApi(logger, repositoryNwo) {
   try {
@@ -150485,6 +150493,26 @@ async function loadPropertiesFromApi(logger, repositoryNwo) {
     );
   }
 }
+async function loadRepositoryProperties(repositoryNwo, logger) {
+  const repositoryOwnerType = github2.context.payload.repository?.owner.type;
+  logger.debug(
+    `Repository owner type is '${repositoryOwnerType ?? "unknown"}'.`
+  );
+  if (repositoryOwnerType === "User") {
+    logger.debug(
+      "Skipping loading repository properties because the repository is owned by a user and therefore cannot have repository properties."
+    );
+    return new Success({});
+  }
+  try {
+    return new Success(await loadPropertiesFromApi(logger, repositoryNwo));
+  } catch (error3) {
+    logger.info(
+      `Failed to load repository properties: ${getErrorMessage(error3)}`
+    );
+    return new Failure(error3);
+  }
+}
 function setProperty2(properties, name, value, logger) {
   const propertyOptions = repositoryPropertyParsers[name];
   if (propertyOptions.validate(value)) {
@@ -150506,6 +150534,15 @@ function parseBooleanRepositoryProperty(name, value, logger) {
 function parseStringRepositoryProperty(_name, value) {
   return value;
 }
+function parseToolsModeRepositoryProperty(name, value, logger) {
+  if (value !== "dynamic" /* Dynamic */ && value !== "enforce" /* Enforce */) {
+    logger.warning(
+      `Repository property '${name}' has unexpected value '${value}'. Expected 'dynamic' or 'enforce'. Defaulting to 'enforce'.`
+    );
+    return "enforce" /* Enforce */;
+  }
+  return value;
+}
 var KNOWN_REPOSITORY_PROPERTY_NAMES = new Set(
   Object.values(RepositoryPropertyName)
 );
@@ -153376,7 +153413,7 @@ async function getCodeQLSource(toolsInput, defaultCliVersion, rawLanguages, useO
         );
       } else {
         if (allowToolcacheValueFF) {
-          logger.warning(
+          logger.info(
             `Ignoring 'tools: ${toolsInput}' because the workflow was not triggered dynamically.`
           );
         } else {
@@ -156717,7 +156754,7 @@ var fs19 = __toESM(require("fs"));
 var path17 = __toESM(require("path"));
 var core14 = __toESM(require_core());
 var toolrunner4 = __toESM(require_toolrunner());
-var github2 = __toESM(require_github());
+var github3 = __toESM(require_github());
 var io6 = __toESM(require_io());
 async function initCodeQL(toolsInput, apiDetails, tempDir, variant, defaultCliVersion, rawLanguages, useOverlayAwareDefaultCliVersion, features, logger) {
   logger.startGroup("Setup CodeQL tools");
@@ -156921,7 +156958,7 @@ function logFileCoverageOnPrsDeprecationWarning(logger) {
   if (process.env["CODEQL_ACTION_DID_LOG_FILE_COVERAGE_ON_PRS_DEPRECATION" /* DID_LOG_FILE_COVERAGE_ON_PRS_DEPRECATION */]) {
     return;
   }
-  const repositoryOwnerType = github2.context.payload.repository?.owner.type;
+  const repositoryOwnerType = github3.context.payload.repository?.owner.type;
   let message = "Starting April 2026, the CodeQL Action will skip computing file coverage information on pull requests to improve analysis performance. File coverage information will still be computed on non-PR analyses.";
   const envVarOptOut = "set the `CODEQL_ACTION_FILE_COVERAGE_ON_PRS` environment variable to `true`.";
   const repoPropertyOptOut = 'create a custom repository property with the name `github-codeql-file-coverage-on-prs` and the type "True/false", then set this property to `true` in the repository\'s settings.';
@@ -158705,10 +158742,50 @@ async function runWrapper3() {
 var fs27 = __toESM(require("fs"));
 var path23 = __toESM(require("path"));
 var core21 = __toESM(require_core());
-var github3 = __toESM(require_github());
 var io7 = __toESM(require_io());
 var semver10 = __toESM(require_semver2());
 
+// src/config/resolve-tools-input.ts
+function resolveToolsInputWithMetadata(toolsWorkflowInput, isDynamicWorkflow2, repositoryProperties, logger) {
+  if (toolsWorkflowInput) {
+    logger.info(
+      `Setting tools: ${toolsWorkflowInput} based on workflow input.`
+    );
+    return {
+      effectiveToolsInput: toolsWorkflowInput,
+      effectiveToolsInputSource: "workflow-input" /* WorkflowInput */,
+      toolsRepoPropertyMode: void 0
+    };
+  }
+  const toolsPropertyValue = repositoryProperties["github-codeql-tools" /* TOOLS */];
+  const toolsMode = repositoryProperties["github-codeql-tools-mode" /* TOOLS_MODE */] ?? "enforce" /* Enforce */;
+  if (toolsPropertyValue && toolsMode === "dynamic" /* Dynamic */ && !isDynamicWorkflow2) {
+    logger.info(
+      `Ignoring '${"github-codeql-tools" /* TOOLS */}' repository property because '${"github-codeql-tools-mode" /* TOOLS_MODE */}' is set to '${toolsMode}' and this is not a dynamic workflow.`
+    );
+    return {
+      effectiveToolsInput: void 0,
+      effectiveToolsInputSource: "none" /* None */,
+      toolsRepoPropertyMode: toolsMode
+    };
+  }
+  if (toolsPropertyValue) {
+    logger.info(
+      `Setting tools: ${toolsPropertyValue} based on the '${"github-codeql-tools" /* TOOLS */}' repository property (mode: '${toolsMode}').`
+    );
+    return {
+      effectiveToolsInput: toolsPropertyValue,
+      effectiveToolsInputSource: "repository-property" /* RepositoryProperty */,
+      toolsRepoPropertyMode: toolsMode
+    };
+  }
+  return {
+    effectiveToolsInput: void 0,
+    effectiveToolsInputSource: "none" /* None */,
+    toolsRepoPropertyMode: void 0
+  };
+}
+
 // src/workflow.ts
 var fs26 = __toESM(require("fs"));
 var path22 = __toESM(require("path"));
@@ -158999,7 +159076,7 @@ async function sendStartingStatusReport(startedAt, config, logger) {
     await sendStatusReport(statusReportBase);
   }
 }
-async function sendCompletedStatusReport2(startedAt, config, configFile, toolsDownloadStatusReport, toolsFeatureFlagsValid, toolsSource, toolsVersion, overlayBaseDatabaseStats, dependencyCachingResults, logger, error3) {
+async function sendCompletedStatusReport2(startedAt, config, configFile, toolsDownloadStatusReport, toolsFeatureFlagsValid, toolsSource, toolsVersion, effectiveToolsInput, effectiveToolsInputSource, toolsRepoPropertyMode, overlayBaseDatabaseStats, dependencyCachingResults, logger, error3) {
   const statusReportBase = await createStatusReportBase(
     "init" /* Init */,
     getActionsStatus(error3),
@@ -159017,6 +159094,9 @@ async function sendCompletedStatusReport2(startedAt, config, configFile, toolsDo
   const initStatusReport = {
     ...statusReportBase,
     tools_input: getOptionalInput("tools") || "",
+    effective_tools_input: effectiveToolsInput || "",
+    effective_tools_input_source: effectiveToolsInputSource,
+    tools_repo_property_mode: toolsRepoPropertyMode || "",
     tools_resolved_version: toolsVersion,
     tools_source: toolsSource || "UNKNOWN" /* Unknown */,
     workflow_languages: workflowLanguages || ""
@@ -159060,6 +159140,9 @@ async function run3(startedAt) {
   let toolsSource;
   let toolsVersion;
   let zstdAvailability;
+  let effectiveToolsInput;
+  let effectiveToolsInputSource = "none" /* None */;
+  let toolsRepoPropertyMode;
   try {
     initializeEnvironment(getActionVersion());
     persistInputs();
@@ -159083,6 +159166,7 @@ async function run3(startedAt) {
       repositoryNwo,
       logger
     );
+    const repositoryProperties = repositoryPropertiesResult.orElse({});
     const jobRunUuid = v4_default();
     logger.info(`Job run UUID is ${jobRunUuid}.`);
     core21.exportVariable("JOB_RUN_UUID" /* JOB_RUN_UUID */, jobRunUuid);
@@ -159108,12 +159192,21 @@ async function run3(startedAt) {
     }
     const codeQLDefaultVersionInfo = await features.getEnabledDefaultCliVersions(gitHubVersion.type);
     toolsFeatureFlagsValid = codeQLDefaultVersionInfo.toolsFeatureFlagsValid;
+    const resolvedToolsInput = resolveToolsInputWithMetadata(
+      getOptionalInput("tools"),
+      isDynamicWorkflow(),
+      repositoryProperties,
+      logger
+    );
+    effectiveToolsInput = resolvedToolsInput.effectiveToolsInput;
+    effectiveToolsInputSource = resolvedToolsInput.effectiveToolsInputSource;
+    toolsRepoPropertyMode = resolvedToolsInput.toolsRepoPropertyMode;
     const rawLanguages = getRawLanguagesNoAutodetect(
       getOptionalInput("languages")
     );
     const useOverlayAwareDefaultCliVersion = analysisKinds?.length === 1 && analysisKinds[0] === "code-scanning" /* CodeScanning */;
     const initCodeQLResult = await initCodeQL(
-      getOptionalInput("tools"),
+      effectiveToolsInput,
       apiDetails,
       getTemporaryDirectory(),
       gitHubVersion.type,
@@ -159149,7 +159242,6 @@ async function run3(startedAt) {
     }
     analysisKinds = await getAnalysisKinds(logger, features);
     const debugMode = getOptionalInput("debug") === "true" || core21.isDebug();
-    const repositoryProperties = repositoryPropertiesResult.orElse({});
     const fileCoverageResult = await getFileCoverageInformationEnabled(
       debugMode,
       codeql,
@@ -159447,6 +159539,9 @@ exec ${goBinaryPath} "$@"`
       toolsFeatureFlagsValid,
       toolsSource,
       toolsVersion,
+      effectiveToolsInput,
+      effectiveToolsInputSource,
+      toolsRepoPropertyMode,
       overlayBaseDatabaseStats,
       dependencyCachingStatus,
       logger,
@@ -159464,31 +159559,14 @@ exec ${goBinaryPath} "$@"`
     toolsFeatureFlagsValid,
     toolsSource,
     toolsVersion,
+    effectiveToolsInput,
+    effectiveToolsInputSource,
+    toolsRepoPropertyMode,
     overlayBaseDatabaseStats,
     dependencyCachingStatus,
     logger
   );
 }
-async function loadRepositoryProperties(repositoryNwo, logger) {
-  const repositoryOwnerType = github3.context.payload.repository?.owner.type;
-  logger.debug(
-    `Repository owner type is '${repositoryOwnerType ?? "unknown"}'.`
-  );
-  if (repositoryOwnerType === "User") {
-    logger.debug(
-      "Skipping loading repository properties because the repository is owned by a user and therefore cannot have repository properties."
-    );
-    return new Success({});
-  }
-  try {
-    return new Success(await loadPropertiesFromApi(logger, repositoryNwo));
-  } catch (error3) {
-    logger.warning(
-      `Failed to load repository properties: ${getErrorMessage(error3)}`
-    );
-    return new Failure(error3);
-  }
-}
 async function recordZstdAvailability(config, zstdAvailability) {
   addNoLanguageDiagnostic(
     config,
@@ -160057,7 +160135,7 @@ async function runWrapper6() {
 
 // src/setup-codeql-action.ts
 var core24 = __toESM(require_core());
-async function sendCompletedStatusReport3(startedAt, toolsDownloadStatusReport, toolsFeatureFlagsValid, toolsSource, toolsVersion, logger, error3) {
+async function sendCompletedStatusReport3(startedAt, toolsDownloadStatusReport, toolsFeatureFlagsValid, toolsSource, toolsVersion, effectiveToolsInput, effectiveToolsInputSource, toolsRepoPropertyMode, logger, error3) {
   const statusReportBase = await createStatusReportBase(
     "setup-codeql" /* SetupCodeQL */,
     getActionsStatus(error3),
@@ -160074,6 +160152,9 @@ async function sendCompletedStatusReport3(startedAt, toolsDownloadStatusReport,
   const initStatusReport = {
     ...statusReportBase,
     tools_input: getOptionalInput("tools") || "",
+    effective_tools_input: effectiveToolsInput || "",
+    effective_tools_input_source: effectiveToolsInputSource,
+    tools_repo_property_mode: toolsRepoPropertyMode || "",
     tools_resolved_version: toolsVersion,
     tools_source: toolsSource || "UNKNOWN" /* Unknown */,
     workflow_languages: ""
@@ -160094,6 +160175,9 @@ async function run6(startedAt) {
   let toolsFeatureFlagsValid;
   let toolsSource;
   let toolsVersion;
+  let effectiveToolsInput;
+  let effectiveToolsInputSource = "none" /* None */;
+  let toolsRepoPropertyMode;
   try {
     initializeEnvironment(getActionVersion());
     const apiDetails = {
@@ -160128,12 +160212,26 @@ async function run6(startedAt) {
     }
     const codeQLDefaultVersionInfo = await features.getEnabledDefaultCliVersions(gitHubVersion.type);
     toolsFeatureFlagsValid = codeQLDefaultVersionInfo.toolsFeatureFlagsValid;
+    const repositoryPropertiesResult = await loadRepositoryProperties(
+      repositoryNwo,
+      logger
+    );
+    const repositoryProperties = repositoryPropertiesResult.orElse({});
+    const resolvedToolsInput = resolveToolsInputWithMetadata(
+      getOptionalInput("tools"),
+      isDynamicWorkflow(),
+      repositoryProperties,
+      logger
+    );
+    effectiveToolsInput = resolvedToolsInput.effectiveToolsInput;
+    effectiveToolsInputSource = resolvedToolsInput.effectiveToolsInputSource;
+    toolsRepoPropertyMode = resolvedToolsInput.toolsRepoPropertyMode;
     const rawLanguages = getRawLanguagesNoAutodetect(
       getOptionalInput("languages")
     );
     const analysisKinds = await getAnalysisKinds(logger, features);
     const initCodeQLResult = await initCodeQL(
-      getOptionalInput("tools"),
+      effectiveToolsInput,
       apiDetails,
       getTemporaryDirectory(),
       gitHubVersion.type,
@@ -160174,6 +160272,9 @@ async function run6(startedAt) {
     toolsFeatureFlagsValid,
     toolsSource,
     toolsVersion,
+    effectiveToolsInput,
+    effectiveToolsInputSource,
+    toolsRepoPropertyMode,
     logger
   );
 }
diff --git a/src/analyze-action.ts b/src/analyze-action.ts
index cc2777bc5f..4b22f2dc55 100644
--- a/src/analyze-action.ts
+++ b/src/analyze-action.ts
@@ -30,7 +30,7 @@ import {
 } from "./dependency-caching";
 import { EnvVar } from "./environment";
 import { initFeatures } from "./feature-flags";
-import { BuiltInLanguage } from "./languages";
+import { BuiltInLanguage } from "./languages/index";
 import { getActionsLogger, Logger } from "./logging";
 import { cleanupAndUploadOverlayBaseDatabaseToCache } from "./overlay/caching";
 import { getRepositoryNwo } from "./repository";
diff --git a/src/analyze.test.ts b/src/analyze.test.ts
index 7523d239bf..e94ea80b57 100644
--- a/src/analyze.test.ts
+++ b/src/analyze.test.ts
@@ -14,7 +14,7 @@ import {
 } from "./analyze";
 import { createStubCodeQL } from "./codeql";
 import { Feature } from "./feature-flags";
-import { BuiltInLanguage } from "./languages";
+import { BuiltInLanguage } from "./languages/index";
 import { getRunnerLogger } from "./logging";
 import {
   setupTests,
diff --git a/src/analyze.ts b/src/analyze.ts
index 63830445d2..0d854cda9d 100644
--- a/src/analyze.ts
+++ b/src/analyze.ts
@@ -21,7 +21,7 @@ import {
 } from "./diff-informed-analysis-utils";
 import { EnvVar } from "./environment";
 import { FeatureEnablement, Feature } from "./feature-flags";
-import { BuiltInLanguage, Language } from "./languages";
+import { BuiltInLanguage, Language } from "./languages/index";
 import { Logger, withGroupAsync } from "./logging";
 import { OverlayDatabaseMode } from "./overlay/overlay-database-mode";
 import type * as sarif from "./sarif";
diff --git a/src/autobuild-action.ts b/src/autobuild-action.ts
index dc20211379..21244340eb 100644
--- a/src/autobuild-action.ts
+++ b/src/autobuild-action.ts
@@ -10,7 +10,7 @@ import { determineAutobuildLanguages, runAutobuild } from "./autobuild";
 import { getCodeQL } from "./codeql";
 import { Config, getConfig } from "./config-utils";
 import { EnvVar } from "./environment";
-import { Language } from "./languages";
+import { Language } from "./languages/index";
 import { Logger, getActionsLogger } from "./logging";
 import {
   StatusReportBase,
diff --git a/src/autobuild.ts b/src/autobuild.ts
index fc4983f4ef..fdf4ef90a8 100644
--- a/src/autobuild.ts
+++ b/src/autobuild.ts
@@ -7,7 +7,7 @@ import * as configUtils from "./config-utils";
 import { DocUrl } from "./doc-url";
 import { EnvVar } from "./environment";
 import { Feature, featureConfig, initFeatures } from "./feature-flags";
-import { BuiltInLanguage, Language } from "./languages";
+import { BuiltInLanguage, Language } from "./languages/index";
 import { Logger } from "./logging";
 import { getRepositoryNwo } from "./repository";
 import { asyncFilter, BuildMode } from "./util";
diff --git a/src/codeql.test.ts b/src/codeql.test.ts
index dea4cf04af..dd9faae92a 100644
--- a/src/codeql.test.ts
+++ b/src/codeql.test.ts
@@ -21,7 +21,7 @@ import {
 import type { Config } from "./config-utils";
 import * as defaults from "./defaults.json";
 import { DocUrl } from "./doc-url";
-import { BuiltInLanguage } from "./languages";
+import { BuiltInLanguage } from "./languages/index";
 import { getRunnerLogger } from "./logging";
 import { ToolsSource } from "./setup-codeql";
 import {
diff --git a/src/codeql.ts b/src/codeql.ts
index 19f933c39a..80e1f1df58 100644
--- a/src/codeql.ts
+++ b/src/codeql.ts
@@ -22,7 +22,7 @@ import {
   FeatureEnablement,
 } from "./feature-flags";
 import { isAnalyzingDefaultBranch } from "./git-utils";
-import { Language } from "./languages";
+import { Language } from "./languages/index";
 import { Logger } from "./logging";
 import { writeBaseDatabaseOidsFile, writeOverlayChangesFile } from "./overlay";
 import { OverlayDatabaseMode } from "./overlay/overlay-database-mode";
diff --git a/src/config-utils.test.ts b/src/config-utils.test.ts
index 10dee55399..79f7b0633e 100644
--- a/src/config-utils.test.ts
+++ b/src/config-utils.test.ts
@@ -18,7 +18,7 @@ import { Feature } from "./feature-flags";
 import { RepositoryProperties } from "./feature-flags/properties";
 import * as gitUtils from "./git-utils";
 import { GitVersionInfo } from "./git-utils";
-import { BuiltInLanguage, Language } from "./languages";
+import { BuiltInLanguage, Language } from "./languages/index";
 import { getRunnerLogger } from "./logging";
 import { CODEQL_OVERLAY_MINIMUM_VERSION } from "./overlay";
 import * as overlayDiagnostics from "./overlay/diagnostics";
diff --git a/src/config-utils.ts b/src/config-utils.ts
index 87329fce2e..b6e5e8ef3c 100644
--- a/src/config-utils.ts
+++ b/src/config-utils.ts
@@ -48,7 +48,7 @@ import {
   hasSubmodules,
   isAnalyzingDefaultBranch,
 } from "./git-utils";
-import { BuiltInLanguage, Language } from "./languages";
+import { BuiltInLanguage, Language } from "./languages/index";
 import { Logger } from "./logging";
 import { CODEQL_OVERLAY_MINIMUM_VERSION } from "./overlay";
 import {
diff --git a/src/config/resolve-tools-input.test.ts b/src/config/resolve-tools-input.test.ts
new file mode 100644
index 0000000000..20c20e5a60
--- /dev/null
+++ b/src/config/resolve-tools-input.test.ts
@@ -0,0 +1,280 @@
+import test from "ava";
+
+import {
+  EffectiveToolsInputSource,
+  resolveToolsInput,
+  resolveToolsInputWithMetadata,
+} from "../config/resolve-tools-input";
+import {
+  RepositoryPropertyName,
+  ToolsModeRepositoryPropertyValue,
+} from "../feature-flags/properties";
+import type { RepositoryProperties } from "../feature-flags/properties";
+import {
+  getRecordingLogger,
+  LoggedMessage,
+  setupTests,
+} from "../testing-utils";
+
+setupTests(test);
+
+test("resolveToolsInput returns undefined when no tools input or repository property is set", (t) => {
+  const loggedMessages: LoggedMessage[] = [];
+  const logger = getRecordingLogger(loggedMessages);
+
+  const result = resolveToolsInput(undefined, false, {}, logger);
+
+  t.is(result, undefined);
+  t.is(loggedMessages.length, 0);
+});
+
+test("resolveToolsInput returns workflow input when only workflow input is provided", (t) => {
+  const loggedMessages: LoggedMessage[] = [];
+  const logger = getRecordingLogger(loggedMessages);
+
+  const result = resolveToolsInput("latest", false, {}, logger);
+
+  t.is(result, "latest");
+  t.is(loggedMessages.length, 1);
+  t.is(
+    loggedMessages[0].message,
+    "Setting tools: latest based on workflow input.",
+  );
+});
+
+test("resolveToolsInput returns repository property when only repository property is provided", (t) => {
+  const loggedMessages: LoggedMessage[] = [];
+  const logger = getRecordingLogger(loggedMessages);
+
+  const repositoryProperties: RepositoryProperties = {
+    [RepositoryPropertyName.TOOLS]: "toolcache",
+  };
+  const result = resolveToolsInput(
+    undefined,
+    false,
+    repositoryProperties,
+    logger,
+  );
+
+  t.is(result, "toolcache");
+  t.is(loggedMessages.length, 1);
+  t.is(
+    loggedMessages[0].message,
+    "Setting tools: toolcache based on the 'github-codeql-tools' repository property (mode: 'enforce').",
+  );
+});
+
+test("resolveToolsInput prioritizes workflow input over repository property", (t) => {
+  const loggedMessages: LoggedMessage[] = [];
+  const logger = getRecordingLogger(loggedMessages);
+
+  const repositoryProperties: RepositoryProperties = {
+    [RepositoryPropertyName.TOOLS]: "toolcache",
+  };
+  const result = resolveToolsInput(
+    "nightly",
+    false,
+    repositoryProperties,
+    logger,
+  );
+
+  t.is(result, "nightly");
+  t.is(loggedMessages.length, 1);
+  t.is(
+    loggedMessages[0].message,
+    "Setting tools: nightly based on workflow input.",
+  );
+});
+
+test("resolveToolsInput treats empty string workflow input as not set", (t) => {
+  const loggedMessages: LoggedMessage[] = [];
+  const logger = getRecordingLogger(loggedMessages);
+
+  const repositoryProperties: RepositoryProperties = {
+    [RepositoryPropertyName.TOOLS]: "toolcache",
+  };
+  const result = resolveToolsInput("", false, repositoryProperties, logger);
+
+  t.is(result, "toolcache");
+  t.is(loggedMessages.length, 1);
+  t.is(
+    loggedMessages[0].message,
+    "Setting tools: toolcache based on the 'github-codeql-tools' repository property (mode: 'enforce').",
+  );
+});
+
+test("resolveToolsInput returns undefined when repository property is undefined", (t) => {
+  const loggedMessages: LoggedMessage[] = [];
+  const logger = getRecordingLogger(loggedMessages);
+
+  const repositoryProperties: RepositoryProperties = {
+    [RepositoryPropertyName.TOOLS]: undefined,
+  };
+  const result = resolveToolsInput(
+    undefined,
+    false,
+    repositoryProperties,
+    logger,
+  );
+
+  t.is(result, undefined);
+  t.is(loggedMessages.length, 0);
+});
+
+test("resolveToolsInput returns repository property when workflow input is not set", (t) => {
+  const loggedMessages: LoggedMessage[] = [];
+  const logger = getRecordingLogger(loggedMessages);
+
+  const repositoryProperties: RepositoryProperties = {
+    [RepositoryPropertyName.TOOLS]: "toolcache",
+  };
+  const result = resolveToolsInput(
+    undefined,
+    false,
+    repositoryProperties,
+    logger,
+  );
+
+  t.is(result, "toolcache");
+  t.is(loggedMessages.length, 1);
+  t.is(
+    loggedMessages[0].message,
+    "Setting tools: toolcache based on the 'github-codeql-tools' repository property (mode: 'enforce').",
+  );
+});
+
+test("resolveToolsInput does not log when workflow input and repository property are not set", (t) => {
+  const loggedMessages: LoggedMessage[] = [];
+  const logger = getRecordingLogger(loggedMessages);
+
+  const result = resolveToolsInput(undefined, false, {}, logger);
+
+  t.is(result, undefined);
+  t.is(loggedMessages.length, 0);
+});
+
+test("resolveToolsInput applies tools property in enforce mode for static workflows", (t) => {
+  const loggedMessages: LoggedMessage[] = [];
+  const logger = getRecordingLogger(loggedMessages);
+
+  const repositoryProperties: RepositoryProperties = {
+    [RepositoryPropertyName.TOOLS]: "toolcache",
+    [RepositoryPropertyName.TOOLS_MODE]:
+      ToolsModeRepositoryPropertyValue.Enforce,
+  };
+  const result = resolveToolsInput(
+    undefined,
+    false,
+    repositoryProperties,
+    logger,
+  );
+
+  t.is(result, "toolcache");
+  t.is(loggedMessages.length, 1);
+  t.is(
+    loggedMessages[0].message,
+    "Setting tools: toolcache based on the 'github-codeql-tools' repository property (mode: 'enforce').",
+  );
+});
+
+test("resolveToolsInput applies tools property in dynamic mode for dynamic workflows", (t) => {
+  const loggedMessages: LoggedMessage[] = [];
+  const logger = getRecordingLogger(loggedMessages);
+
+  const repositoryProperties: RepositoryProperties = {
+    [RepositoryPropertyName.TOOLS]: "toolcache",
+    [RepositoryPropertyName.TOOLS_MODE]:
+      ToolsModeRepositoryPropertyValue.Dynamic,
+  };
+  const result = resolveToolsInput(
+    undefined,
+    true,
+    repositoryProperties,
+    logger,
+  );
+
+  t.is(result, "toolcache");
+  t.is(loggedMessages.length, 1);
+  t.is(
+    loggedMessages[0].message,
+    "Setting tools: toolcache based on the 'github-codeql-tools' repository property (mode: 'dynamic').",
+  );
+});
+
+test("resolveToolsInput ignores tools property in dynamic mode for static workflows", (t) => {
+  const loggedMessages: LoggedMessage[] = [];
+  const logger = getRecordingLogger(loggedMessages);
+
+  const repositoryProperties: RepositoryProperties = {
+    [RepositoryPropertyName.TOOLS]: "toolcache",
+    [RepositoryPropertyName.TOOLS_MODE]:
+      ToolsModeRepositoryPropertyValue.Dynamic,
+  };
+  const result = resolveToolsInput(
+    undefined,
+    false,
+    repositoryProperties,
+    logger,
+  );
+
+  t.is(result, undefined);
+  t.is(loggedMessages.length, 1);
+  t.is(
+    loggedMessages[0].message,
+    "Ignoring 'github-codeql-tools' repository property because 'github-codeql-tools-mode' is set to 'dynamic' and this is not a dynamic workflow.",
+  );
+});
+
+test("resolveToolsInputWithMetadata reports workflow input source", (t) => {
+  const logger = getRecordingLogger([]);
+
+  const result = resolveToolsInputWithMetadata("latest", false, {}, logger);
+
+  t.is(result.effectiveToolsInput, "latest");
+  t.is(
+    result.effectiveToolsInputSource,
+    EffectiveToolsInputSource.WorkflowInput,
+  );
+  t.is(result.toolsRepoPropertyMode, undefined);
+});
+
+test("resolveToolsInputWithMetadata reports repository property source and mode", (t) => {
+  const logger = getRecordingLogger([]);
+
+  const result = resolveToolsInputWithMetadata(
+    undefined,
+    false,
+    {
+      [RepositoryPropertyName.TOOLS]: "toolcache",
+      [RepositoryPropertyName.TOOLS_MODE]:
+        ToolsModeRepositoryPropertyValue.Enforce,
+    },
+    logger,
+  );
+
+  t.is(result.effectiveToolsInput, "toolcache");
+  t.is(
+    result.effectiveToolsInputSource,
+    EffectiveToolsInputSource.RepositoryProperty,
+  );
+  t.is(result.toolsRepoPropertyMode, ToolsModeRepositoryPropertyValue.Enforce);
+});
+
+test("resolveToolsInputWithMetadata reports dynamic-mode skip on static workflows", (t) => {
+  const logger = getRecordingLogger([]);
+
+  const result = resolveToolsInputWithMetadata(
+    undefined,
+    false,
+    {
+      [RepositoryPropertyName.TOOLS]: "toolcache",
+      [RepositoryPropertyName.TOOLS_MODE]:
+        ToolsModeRepositoryPropertyValue.Dynamic,
+    },
+    logger,
+  );
+
+  t.is(result.effectiveToolsInput, undefined);
+  t.is(result.effectiveToolsInputSource, EffectiveToolsInputSource.None);
+  t.is(result.toolsRepoPropertyMode, ToolsModeRepositoryPropertyValue.Dynamic);
+});
diff --git a/src/config/resolve-tools-input.ts b/src/config/resolve-tools-input.ts
new file mode 100644
index 0000000000..06f0ec126c
--- /dev/null
+++ b/src/config/resolve-tools-input.ts
@@ -0,0 +1,100 @@
+import {
+  RepositoryProperties,
+  RepositoryPropertyName,
+  ToolsModeRepositoryPropertyValue,
+} from "../feature-flags/properties";
+import { Logger } from "../logging";
+
+export enum EffectiveToolsInputSource {
+  WorkflowInput = "workflow-input",
+  RepositoryProperty = "repository-property",
+  None = "none",
+}
+
+export type ResolvedToolsInput = {
+  effectiveToolsInput: string | undefined;
+  effectiveToolsInputSource: EffectiveToolsInputSource;
+  toolsRepoPropertyMode: ToolsModeRepositoryPropertyValue | undefined;
+};
+
+/**
+ * Resolves the effective tools input by combining the workflow input and repository properties.
+ * The explicit `tools` workflow input takes precedence. If none is provided,
+ * falls back to the repository property (if set). The optional
+ * `github-codeql-tools-mode` repository property controls whether this fallback
+ * applies to all workflows (`enforce`) or only dynamic workflows (`dynamic`).
+ *
+ * @param toolsWorkflowInput - The value of the `tools` workflow input, if provided.
+ * @param isDynamicWorkflow - Whether the current workflow is dynamic.
+ * @param repositoryProperties - The parsed repository properties.
+ * @param logger - Logger for outputting resolution messages.
+ * @returns The effective tools input value.
+ */
+export function resolveToolsInput(
+  toolsWorkflowInput: string | undefined,
+  isDynamicWorkflow: boolean,
+  repositoryProperties: RepositoryProperties,
+  logger: Logger,
+): string | undefined {
+  return resolveToolsInputWithMetadata(
+    toolsWorkflowInput,
+    isDynamicWorkflow,
+    repositoryProperties,
+    logger,
+  ).effectiveToolsInput;
+}
+
+export function resolveToolsInputWithMetadata(
+  toolsWorkflowInput: string | undefined,
+  isDynamicWorkflow: boolean,
+  repositoryProperties: RepositoryProperties,
+  logger: Logger,
+): ResolvedToolsInput {
+  if (toolsWorkflowInput) {
+    logger.info(
+      `Setting tools: ${toolsWorkflowInput} based on workflow input.`,
+    );
+    return {
+      effectiveToolsInput: toolsWorkflowInput,
+      effectiveToolsInputSource: EffectiveToolsInputSource.WorkflowInput,
+      toolsRepoPropertyMode: undefined,
+    };
+  }
+
+  const toolsPropertyValue = repositoryProperties[RepositoryPropertyName.TOOLS];
+  const toolsMode =
+    repositoryProperties[RepositoryPropertyName.TOOLS_MODE] ??
+    ToolsModeRepositoryPropertyValue.Enforce;
+
+  if (
+    toolsPropertyValue &&
+    toolsMode === ToolsModeRepositoryPropertyValue.Dynamic &&
+    !isDynamicWorkflow
+  ) {
+    logger.info(
+      `Ignoring '${RepositoryPropertyName.TOOLS}' repository property because '${RepositoryPropertyName.TOOLS_MODE}' is set to '${toolsMode}' and this is not a dynamic workflow.`,
+    );
+    return {
+      effectiveToolsInput: undefined,
+      effectiveToolsInputSource: EffectiveToolsInputSource.None,
+      toolsRepoPropertyMode: toolsMode,
+    };
+  }
+
+  if (toolsPropertyValue) {
+    logger.info(
+      `Setting tools: ${toolsPropertyValue} based on the '${RepositoryPropertyName.TOOLS}' repository property (mode: '${toolsMode}').`,
+    );
+    return {
+      effectiveToolsInput: toolsPropertyValue,
+      effectiveToolsInputSource: EffectiveToolsInputSource.RepositoryProperty,
+      toolsRepoPropertyMode: toolsMode,
+    };
+  }
+
+  return {
+    effectiveToolsInput: undefined,
+    effectiveToolsInputSource: EffectiveToolsInputSource.None,
+    toolsRepoPropertyMode: undefined,
+  };
+}
diff --git a/src/database-upload.test.ts b/src/database-upload.test.ts
index 1cfbaecad6..45be8b5d26 100644
--- a/src/database-upload.test.ts
+++ b/src/database-upload.test.ts
@@ -12,7 +12,7 @@ import { createStubCodeQL } from "./codeql";
 import { Config } from "./config-utils";
 import { cleanupAndUploadDatabases } from "./database-upload";
 import * as gitUtils from "./git-utils";
-import { BuiltInLanguage } from "./languages";
+import { BuiltInLanguage } from "./languages/index";
 import { RepositoryNwo } from "./repository";
 import {
   checkExpectedLogMessages,
diff --git a/src/debug-artifacts.ts b/src/debug-artifacts.ts
index 016fcdf7c4..2f97721547 100644
--- a/src/debug-artifacts.ts
+++ b/src/debug-artifacts.ts
@@ -13,7 +13,7 @@ import { type CodeQL } from "./codeql";
 import { Config } from "./config-utils";
 import { EnvVar } from "./environment";
 import * as json from "./json";
-import { Language } from "./languages";
+import { Language } from "./languages/index";
 import { Logger, withGroup } from "./logging";
 import {
   isSafeArtifactUpload,
diff --git a/src/dependency-caching.test.ts b/src/dependency-caching.test.ts
index e611cd03eb..944f12c3c4 100644
--- a/src/dependency-caching.test.ts
+++ b/src/dependency-caching.test.ts
@@ -27,7 +27,7 @@ import {
   CacheStoreResult,
 } from "./dependency-caching";
 import { Feature } from "./feature-flags";
-import { BuiltInLanguage } from "./languages";
+import { BuiltInLanguage } from "./languages/index";
 import {
   setupTests,
   createFeatures,
diff --git a/src/dependency-caching.ts b/src/dependency-caching.ts
index f04d38f46c..fa8ff7b13e 100644
--- a/src/dependency-caching.ts
+++ b/src/dependency-caching.ts
@@ -11,7 +11,7 @@ import { CodeQL } from "./codeql";
 import { Config } from "./config-utils";
 import { EnvVar } from "./environment";
 import { Feature, FeatureEnablement } from "./feature-flags";
-import { BuiltInLanguage, Language } from "./languages";
+import { BuiltInLanguage, Language } from "./languages/index";
 import { Logger } from "./logging";
 import { getErrorMessage, getRequiredEnvParam } from "./util";
 
diff --git a/src/diagnostics.ts b/src/diagnostics.ts
index 65e82ce1af..5bad57229b 100644
--- a/src/diagnostics.ts
+++ b/src/diagnostics.ts
@@ -2,7 +2,7 @@ import { existsSync, mkdirSync, writeFileSync } from "fs";
 import path from "path";
 
 import type { Config } from "./config-utils";
-import { Language } from "./languages";
+import { Language } from "./languages/index";
 import { getActionsLogger } from "./logging";
 import { getCodeQLDatabasePath } from "./util";
 
diff --git a/src/feature-flags/properties.test.ts b/src/feature-flags/properties.test.ts
index 2676c2dcda..f8b088aa5b 100644
--- a/src/feature-flags/properties.test.ts
+++ b/src/feature-flags/properties.test.ts
@@ -78,6 +78,8 @@ test.serial("loadPropertiesFromApi loads known properties", async (t) => {
     url: "",
     data: [
       { property_name: "github-codeql-extra-queries", value: "+queries" },
+      { property_name: "github-codeql-tools", value: "toolcache" },
+      { property_name: "github-codeql-tools-mode", value: "dynamic" },
       { property_name: "unknown-property", value: "something" },
     ] satisfies properties.GitHubPropertiesResponse,
   });
@@ -87,9 +89,45 @@ test.serial("loadPropertiesFromApi loads known properties", async (t) => {
     logger,
     mockRepositoryNwo,
   );
-  t.deepEqual(response, { "github-codeql-extra-queries": "+queries" });
+  t.deepEqual(response, {
+    "github-codeql-extra-queries": "+queries",
+    "github-codeql-tools": "toolcache",
+    "github-codeql-tools-mode": "dynamic",
+  });
 });
 
+test.serial(
+  "loadPropertiesFromApi warns if tools mode property has unexpected value",
+  async (t) => {
+    sinon.stub(api, "getRepositoryProperties").resolves({
+      headers: {},
+      status: 200,
+      url: "",
+      data: [
+        {
+          property_name: "github-codeql-tools-mode",
+          value: "all",
+        },
+      ] satisfies properties.GitHubPropertiesResponse,
+    });
+    const logger = getRunnerLogger(true);
+    const warningSpy = sinon.spy(logger, "warning");
+    const mockRepositoryNwo = parseRepositoryNwo("owner/repo");
+    const response = await properties.loadPropertiesFromApi(
+      logger,
+      mockRepositoryNwo,
+    );
+    t.deepEqual(response, {
+      "github-codeql-tools-mode": "enforce",
+    });
+    t.true(warningSpy.calledOnce);
+    t.is(
+      warningSpy.firstCall.args[0],
+      "Repository property 'github-codeql-tools-mode' has unexpected value 'all'. Expected 'dynamic' or 'enforce'. Defaulting to 'enforce'.",
+    );
+  },
+);
+
 test.serial("loadPropertiesFromApi parses true boolean property", async (t) => {
   sinon.stub(api, "getRepositoryProperties").resolves({
     headers: {},
diff --git a/src/feature-flags/properties.ts b/src/feature-flags/properties.ts
index 12ba280bec..b27ee414ce 100644
--- a/src/feature-flags/properties.ts
+++ b/src/feature-flags/properties.ts
@@ -1,7 +1,10 @@
+import * as github from "@actions/github";
+
 import { isDynamicWorkflow } from "../actions-util";
 import { getRepositoryProperties } from "../api-client";
 import { Logger } from "../logging";
 import { RepositoryNwo } from "../repository";
+import { getErrorMessage, Result, Success, Failure } from "../util";
 
 /** The common prefix that we expect all of our repository properties to have. */
 export const GITHUB_CODEQL_PROPERTY_PREFIX = "github-codeql-";
@@ -13,6 +16,13 @@ export enum RepositoryPropertyName {
   DISABLE_OVERLAY = "github-codeql-disable-overlay",
   EXTRA_QUERIES = "github-codeql-extra-queries",
   FILE_COVERAGE_ON_PRS = "github-codeql-file-coverage-on-prs",
+  TOOLS = "github-codeql-tools",
+  TOOLS_MODE = "github-codeql-tools-mode",
+}
+
+export enum ToolsModeRepositoryPropertyValue {
+  Dynamic = "dynamic",
+  Enforce = "enforce",
 }
 
 /** Parsed types of the known repository properties. */
@@ -20,6 +30,8 @@ export type AllRepositoryProperties = {
   [RepositoryPropertyName.DISABLE_OVERLAY]: boolean;
   [RepositoryPropertyName.EXTRA_QUERIES]: string;
   [RepositoryPropertyName.FILE_COVERAGE_ON_PRS]: boolean;
+  [RepositoryPropertyName.TOOLS]: string;
+  [RepositoryPropertyName.TOOLS_MODE]: ToolsModeRepositoryPropertyValue;
 };
 
 /** Parsed repository properties. */
@@ -30,6 +42,8 @@ export type RepositoryPropertyApiType = {
   [RepositoryPropertyName.DISABLE_OVERLAY]: string;
   [RepositoryPropertyName.EXTRA_QUERIES]: string;
   [RepositoryPropertyName.FILE_COVERAGE_ON_PRS]: string;
+  [RepositoryPropertyName.TOOLS]: string;
+  [RepositoryPropertyName.TOOLS_MODE]: string;
 };
 
 /** The type of functions which take the `value` from the API and try to convert it to the type we want. */
@@ -77,6 +91,11 @@ const repositoryPropertyParsers: {
   [RepositoryPropertyName.DISABLE_OVERLAY]: booleanProperty,
   [RepositoryPropertyName.EXTRA_QUERIES]: stringProperty,
   [RepositoryPropertyName.FILE_COVERAGE_ON_PRS]: booleanProperty,
+  [RepositoryPropertyName.TOOLS]: stringProperty,
+  [RepositoryPropertyName.TOOLS_MODE]: {
+    validate: isString,
+    parse: parseToolsModeRepositoryProperty,
+  },
 };
 
 /**
@@ -172,6 +191,38 @@ export async function loadPropertiesFromApi(
   }
 }
 
+/**
+ * Loads [repository properties](https://docs.github.com/en/organizations/managing-organization-settings/managing-custom-properties-for-repositories-in-your-organization) if applicable.
+ */
+export async function loadRepositoryProperties(
+  repositoryNwo: RepositoryNwo,
+  logger: Logger,
+): Promise<Result<RepositoryProperties, unknown>> {
+  // See if we can skip loading repository properties early. In particular,
+  // repositories owned by users cannot have repository properties, so we can
+  // skip the API call entirely in that case.
+  const repositoryOwnerType = github.context.payload.repository?.owner.type;
+  logger.debug(
+    `Repository owner type is '${repositoryOwnerType ?? "unknown"}'.`,
+  );
+  if (repositoryOwnerType === "User") {
+    logger.debug(
+      "Skipping loading repository properties because the repository is owned by a user and " +
+        "therefore cannot have repository properties.",
+    );
+    return new Success({});
+  }
+
+  try {
+    return new Success(await loadPropertiesFromApi(logger, repositoryNwo));
+  } catch (error) {
+    logger.info(
+      `Failed to load repository properties: ${getErrorMessage(error)}`,
+    );
+    return new Failure(error);
+  }
+}
+
 /**
  * Validate that `value` has the correct type for `K` and, if so, update the partial set of repository
  * properties with the parsed value of the specified property.
@@ -217,6 +268,25 @@ function parseStringRepositoryProperty(_name: string, value: string): string {
   return value;
 }
 
+/** Parse the tools mode repository property. */
+function parseToolsModeRepositoryProperty(
+  name: string,
+  value: string,
+  logger: Logger,
+): ToolsModeRepositoryPropertyValue {
+  if (
+    value !== ToolsModeRepositoryPropertyValue.Dynamic &&
+    value !== ToolsModeRepositoryPropertyValue.Enforce
+  ) {
+    logger.warning(
+      `Repository property '${name}' has unexpected value '${value}'. Expected 'dynamic' or 'enforce'. Defaulting to 'enforce'.`,
+    );
+    return ToolsModeRepositoryPropertyValue.Enforce;
+  }
+
+  return value;
+}
+
 /** Set of known repository property names, for fast lookups. */
 const KNOWN_REPOSITORY_PROPERTY_NAMES = new Set<string>(
   Object.values(RepositoryPropertyName),
diff --git a/src/init-action.ts b/src/init-action.ts
index 9d2619b1d1..747871b090 100644
--- a/src/init-action.ts
+++ b/src/init-action.ts
@@ -2,12 +2,12 @@ import * as fs from "fs";
 import * as path from "path";
 
 import * as core from "@actions/core";
-import * as github from "@actions/github";
 import * as io from "@actions/io";
 import * as semver from "semver";
 import { v4 as uuidV4 } from "uuid";
 
 import {
+  isDynamicWorkflow,
   FileCmdNotFoundError,
   getActionVersion,
   getFileType,
@@ -24,6 +24,10 @@ import {
   shouldRestoreCache,
 } from "./caching-utils";
 import { CodeQL } from "./codeql";
+import {
+  EffectiveToolsInputSource,
+  resolveToolsInputWithMetadata,
+} from "./config/resolve-tools-input";
 import * as configUtils from "./config-utils";
 import {
   DependencyCacheRestoreStatusReport,
@@ -40,8 +44,8 @@ import {
 import { EnvVar } from "./environment";
 import { Feature, FeatureEnablement, initFeatures } from "./feature-flags";
 import {
-  loadPropertiesFromApi,
-  RepositoryProperties,
+  loadRepositoryProperties,
+  ToolsModeRepositoryPropertyValue,
 } from "./feature-flags/properties";
 import {
   checkInstallPython311,
@@ -53,14 +57,14 @@ import {
   initConfig,
   runDatabaseInitCluster,
 } from "./init";
-import { JavaEnvVars, BuiltInLanguage } from "./languages";
+import { JavaEnvVars, BuiltInLanguage } from "./languages/index";
 import { getActionsLogger, Logger, withGroupAsync } from "./logging";
 import {
   downloadOverlayBaseDatabaseFromCache,
   OverlayBaseDatabaseDownloadStats,
 } from "./overlay/caching";
 import { OverlayDatabaseMode } from "./overlay/overlay-database-mode";
-import { getRepositoryNwo, RepositoryNwo } from "./repository";
+import { getRepositoryNwo } from "./repository";
 import { ToolsSource } from "./setup-codeql";
 import {
   ActionName,
@@ -93,10 +97,7 @@ import {
   checkActionVersion,
   getErrorMessage,
   BuildMode,
-  Result,
   getOptionalEnvVar,
-  Success,
-  Failure,
 } from "./util";
 import { checkWorkflow } from "./workflow";
 
@@ -140,6 +141,9 @@ async function sendCompletedStatusReport(
   toolsFeatureFlagsValid: boolean | undefined,
   toolsSource: ToolsSource,
   toolsVersion: string,
+  effectiveToolsInput: string | undefined,
+  effectiveToolsInputSource: EffectiveToolsInputSource,
+  toolsRepoPropertyMode: ToolsModeRepositoryPropertyValue | undefined,
   overlayBaseDatabaseStats: OverlayBaseDatabaseDownloadStats | undefined,
   dependencyCachingResults: DependencyCacheRestoreStatusReport | undefined,
   logger: Logger,
@@ -165,6 +169,9 @@ async function sendCompletedStatusReport(
   const initStatusReport: InitStatusReport = {
     ...statusReportBase,
     tools_input: getOptionalInput("tools") || "",
+    effective_tools_input: effectiveToolsInput || "",
+    effective_tools_input_source: effectiveToolsInputSource,
+    tools_repo_property_mode: toolsRepoPropertyMode || "",
     tools_resolved_version: toolsVersion,
     tools_source: toolsSource || ToolsSource.Unknown,
     workflow_languages: workflowLanguages || "",
@@ -219,6 +226,9 @@ async function run(startedAt: Date) {
   let toolsSource: ToolsSource;
   let toolsVersion: string;
   let zstdAvailability: ZstdAvailability | undefined;
+  let effectiveToolsInput: string | undefined;
+  let effectiveToolsInputSource: EffectiveToolsInputSource;
+  let toolsRepoPropertyMode: ToolsModeRepositoryPropertyValue | undefined;
 
   try {
     initializeEnvironment(getActionVersion());
@@ -251,6 +261,7 @@ async function run(startedAt: Date) {
       repositoryNwo,
       logger,
     );
+    const repositoryProperties = repositoryPropertiesResult.orElse({});
 
     // Create a unique identifier for this run.
     const jobRunUuid = uuidV4();
@@ -296,6 +307,21 @@ async function run(startedAt: Date) {
     const codeQLDefaultVersionInfo =
       await features.getEnabledDefaultCliVersions(gitHubVersion.type);
     toolsFeatureFlagsValid = codeQLDefaultVersionInfo.toolsFeatureFlagsValid;
+
+    // Determine the effective tools input.
+    // The explicit `tools` workflow input takes precedence. If none is provided,
+    // fall back to the 'github-codeql-tools' repository property (if set).
+    // If 'github-codeql-tools-mode' is set to 'dynamic', this fallback applies
+    // only to dynamic workflows. Otherwise, it applies to all workflows.
+    const resolvedToolsInput = resolveToolsInputWithMetadata(
+      getOptionalInput("tools"),
+      isDynamicWorkflow(),
+      repositoryProperties,
+      logger,
+    );
+    effectiveToolsInput = resolvedToolsInput.effectiveToolsInput;
+    effectiveToolsInputSource = resolvedToolsInput.effectiveToolsInputSource;
+    toolsRepoPropertyMode = resolvedToolsInput.toolsRepoPropertyMode;
     const rawLanguages = configUtils.getRawLanguagesNoAutodetect(
       getOptionalInput("languages"),
     );
@@ -303,7 +329,7 @@ async function run(startedAt: Date) {
       analysisKinds?.length === 1 &&
       analysisKinds[0] === AnalysisKind.CodeScanning;
     const initCodeQLResult = await initCodeQL(
-      getOptionalInput("tools"),
+      effectiveToolsInput,
       apiDetails,
       getTemporaryDirectory(),
       gitHubVersion.type,
@@ -350,7 +376,6 @@ async function run(startedAt: Date) {
 
     analysisKinds = await getAnalysisKinds(logger, features);
     const debugMode = getOptionalInput("debug") === "true" || core.isDebug();
-    const repositoryProperties = repositoryPropertiesResult.orElse({});
     const fileCoverageResult = await getFileCoverageInformationEnabled(
       debugMode,
       codeql,
@@ -769,6 +794,9 @@ async function run(startedAt: Date) {
       toolsFeatureFlagsValid,
       toolsSource,
       toolsVersion,
+      effectiveToolsInput,
+      effectiveToolsInputSource,
+      toolsRepoPropertyMode,
       overlayBaseDatabaseStats,
       dependencyCachingStatus,
       logger,
@@ -786,44 +814,15 @@ async function run(startedAt: Date) {
     toolsFeatureFlagsValid,
     toolsSource,
     toolsVersion,
+    effectiveToolsInput,
+    effectiveToolsInputSource,
+    toolsRepoPropertyMode,
     overlayBaseDatabaseStats,
     dependencyCachingStatus,
     logger,
   );
 }
 
-/**
- * Loads [repository properties](https://docs.github.com/en/organizations/managing-organization-settings/managing-custom-properties-for-repositories-in-your-organization) if applicable.
- */
-async function loadRepositoryProperties(
-  repositoryNwo: RepositoryNwo,
-  logger: Logger,
-): Promise<Result<RepositoryProperties, unknown>> {
-  // See if we can skip loading repository properties early. In particular,
-  // repositories owned by users cannot have repository properties, so we can
-  // skip the API call entirely in that case.
-  const repositoryOwnerType = github.context.payload.repository?.owner.type;
-  logger.debug(
-    `Repository owner type is '${repositoryOwnerType ?? "unknown"}'.`,
-  );
-  if (repositoryOwnerType === "User") {
-    logger.debug(
-      "Skipping loading repository properties because the repository is owned by a user and " +
-        "therefore cannot have repository properties.",
-    );
-    return new Success({});
-  }
-
-  try {
-    return new Success(await loadPropertiesFromApi(logger, repositoryNwo));
-  } catch (error) {
-    logger.warning(
-      `Failed to load repository properties: ${getErrorMessage(error)}`,
-    );
-    return new Failure(error);
-  }
-}
-
 async function recordZstdAvailability(
   config: configUtils.Config,
   zstdAvailability: ZstdAvailability,
diff --git a/src/init.test.ts b/src/init.test.ts
index 88ad0c9b18..e92424fd7c 100644
--- a/src/init.test.ts
+++ b/src/init.test.ts
@@ -15,7 +15,7 @@ import {
   getFileCoverageInformationEnabled,
   logFileCoverageOnPrsDeprecationWarning,
 } from "./init";
-import { BuiltInLanguage } from "./languages";
+import { BuiltInLanguage } from "./languages/index";
 import {
   createFeatures,
   LoggedMessage,
diff --git a/src/init.ts b/src/init.ts
index 2533d9a894..e88f825249 100644
--- a/src/init.ts
+++ b/src/init.ts
@@ -26,7 +26,7 @@ import {
   RepositoryProperties,
   RepositoryPropertyName,
 } from "./feature-flags/properties";
-import { BuiltInLanguage, Language } from "./languages";
+import { BuiltInLanguage, Language } from "./languages/index";
 import { Logger, withGroupAsync } from "./logging";
 import { ToolsSource } from "./setup-codeql";
 import { ZstdAvailability } from "./tar";
diff --git a/src/setup-codeql-action.ts b/src/setup-codeql-action.ts
index d3e0e7dbcc..2e25d30587 100644
--- a/src/setup-codeql-action.ts
+++ b/src/setup-codeql-action.ts
@@ -2,6 +2,7 @@ import * as core from "@actions/core";
 import { v4 as uuidV4 } from "uuid";
 
 import {
+  isDynamicWorkflow,
   getActionVersion,
   getOptionalInput,
   getRequiredInput,
@@ -10,9 +11,17 @@ import {
 import { AnalysisKind, getAnalysisKinds } from "./analyses";
 import { getGitHubVersion } from "./api-client";
 import { CodeQL } from "./codeql";
+import {
+  EffectiveToolsInputSource,
+  resolveToolsInputWithMetadata,
+} from "./config/resolve-tools-input";
 import { getRawLanguagesNoAutodetect } from "./config-utils";
 import { EnvVar } from "./environment";
 import { initFeatures } from "./feature-flags";
+import {
+  loadRepositoryProperties,
+  ToolsModeRepositoryPropertyValue,
+} from "./feature-flags/properties";
 import { initCodeQL } from "./init";
 import { getActionsLogger, Logger } from "./logging";
 import { getRepositoryNwo } from "./repository";
@@ -48,6 +57,9 @@ async function sendCompletedStatusReport(
   toolsFeatureFlagsValid: boolean | undefined,
   toolsSource: ToolsSource,
   toolsVersion: string,
+  effectiveToolsInput: string | undefined,
+  effectiveToolsInputSource: EffectiveToolsInputSource,
+  toolsRepoPropertyMode: ToolsModeRepositoryPropertyValue | undefined,
   logger: Logger,
   error?: Error,
 ): Promise<void> {
@@ -69,6 +81,9 @@ async function sendCompletedStatusReport(
   const initStatusReport: InitStatusReport = {
     ...statusReportBase,
     tools_input: getOptionalInput("tools") || "",
+    effective_tools_input: effectiveToolsInput || "",
+    effective_tools_input_source: effectiveToolsInputSource,
+    tools_repo_property_mode: toolsRepoPropertyMode || "",
     tools_resolved_version: toolsVersion,
     tools_source: toolsSource || ToolsSource.Unknown,
     workflow_languages: "",
@@ -99,6 +114,9 @@ async function run(startedAt: Date): Promise<void> {
   let toolsFeatureFlagsValid: boolean | undefined;
   let toolsSource: ToolsSource;
   let toolsVersion: string;
+  let effectiveToolsInput: string | undefined;
+  let effectiveToolsInputSource: EffectiveToolsInputSource;
+  let toolsRepoPropertyMode: ToolsModeRepositoryPropertyValue | undefined;
 
   try {
     initializeEnvironment(getActionVersion());
@@ -141,12 +159,35 @@ async function run(startedAt: Date): Promise<void> {
     const codeQLDefaultVersionInfo =
       await features.getEnabledDefaultCliVersions(gitHubVersion.type);
     toolsFeatureFlagsValid = codeQLDefaultVersionInfo.toolsFeatureFlagsValid;
+
+    // Fetch the values of known repository properties that affect us.
+    const repositoryPropertiesResult = await loadRepositoryProperties(
+      repositoryNwo,
+      logger,
+    );
+    const repositoryProperties = repositoryPropertiesResult.orElse({});
+
+    // Determine the effective tools input.
+    // The explicit `tools` workflow input takes precedence. If none is provided,
+    // fall back to the 'github-codeql-tools' repository property (if set).
+    // If 'github-codeql-tools-mode' is set to 'dynamic', this fallback applies
+    // only to dynamic workflows. Otherwise, it applies to all workflows.
+    const resolvedToolsInput = resolveToolsInputWithMetadata(
+      getOptionalInput("tools"),
+      isDynamicWorkflow(),
+      repositoryProperties,
+      logger,
+    );
+    effectiveToolsInput = resolvedToolsInput.effectiveToolsInput;
+    effectiveToolsInputSource = resolvedToolsInput.effectiveToolsInputSource;
+    toolsRepoPropertyMode = resolvedToolsInput.toolsRepoPropertyMode;
     const rawLanguages = getRawLanguagesNoAutodetect(
       getOptionalInput("languages"),
     );
     const analysisKinds = await getAnalysisKinds(logger, features);
+
     const initCodeQLResult = await initCodeQL(
-      getOptionalInput("tools"),
+      effectiveToolsInput,
       apiDetails,
       getTemporaryDirectory(),
       gitHubVersion.type,
@@ -191,6 +232,9 @@ async function run(startedAt: Date): Promise<void> {
     toolsFeatureFlagsValid,
     toolsSource,
     toolsVersion,
+    effectiveToolsInput,
+    effectiveToolsInputSource,
+    toolsRepoPropertyMode,
     logger,
   );
 }
diff --git a/src/setup-codeql.ts b/src/setup-codeql.ts
index 3db0b6ca4d..c654ba27a7 100644
--- a/src/setup-codeql.ts
+++ b/src/setup-codeql.ts
@@ -559,7 +559,7 @@ export async function getCodeQLSource(
         );
       } else {
         if (allowToolcacheValueFF) {
-          logger.warning(
+          logger.info(
             `Ignoring 'tools: ${toolsInput}' because the workflow was not triggered dynamically.`,
           );
         } else {
diff --git a/src/start-proxy-action.ts b/src/start-proxy-action.ts
index 609b576441..e3750af8ae 100644
--- a/src/start-proxy-action.ts
+++ b/src/start-proxy-action.ts
@@ -6,7 +6,7 @@ import * as core from "@actions/core";
 import * as actionsUtil from "./actions-util";
 import { getGitHubVersion } from "./api-client";
 import { Feature, FeatureEnablement, initFeatures } from "./feature-flags";
-import { BuiltInLanguage, parseBuiltInLanguage } from "./languages";
+import { BuiltInLanguage, parseBuiltInLanguage } from "./languages/index";
 import { getActionsLogger, Logger } from "./logging";
 import { getRepositoryNwo } from "./repository";
 import {
diff --git a/src/start-proxy.test.ts b/src/start-proxy.test.ts
index 9f12656f62..57822923f8 100644
--- a/src/start-proxy.test.ts
+++ b/src/start-proxy.test.ts
@@ -10,7 +10,7 @@ import * as defaults from "./defaults.json";
 import { setUpFeatureFlagTests } from "./feature-flags/testing-util";
 import { UnvalidatedObject, validateSchema } from "./json";
 import { makeFromSchema } from "./json/testing-util";
-import { BuiltInLanguage } from "./languages";
+import { BuiltInLanguage } from "./languages/index";
 import { getRunnerLogger, Logger } from "./logging";
 import * as startProxyExports from "./start-proxy";
 import * as statusReport from "./status-report";
diff --git a/src/start-proxy.ts b/src/start-proxy.ts
index d6111510f6..3a123a7bb5 100644
--- a/src/start-proxy.ts
+++ b/src/start-proxy.ts
@@ -18,7 +18,7 @@ import {
   FeatureEnablement,
 } from "./feature-flags";
 import * as json from "./json";
-import { BuiltInLanguage } from "./languages";
+import { BuiltInLanguage } from "./languages/index";
 import { Logger } from "./logging";
 import {
   Address,
diff --git a/src/status-report.test.ts b/src/status-report.test.ts
index 52132b7649..0455eedd6e 100644
--- a/src/status-report.test.ts
+++ b/src/status-report.test.ts
@@ -2,9 +2,10 @@ import test from "ava";
 import * as sinon from "sinon";
 
 import * as actionsUtil from "./actions-util";
+import { EffectiveToolsInputSource } from "./config/resolve-tools-input";
 import { Config } from "./config-utils";
 import { EnvVar } from "./environment";
-import { BuiltInLanguage } from "./languages";
+import { BuiltInLanguage } from "./languages/index";
 import { getRunnerLogger } from "./logging";
 import { ToolsSource } from "./setup-codeql";
 import {
@@ -316,6 +317,9 @@ const testCreateInitWithConfigStatusReport = makeMacro({
         const initStatusReport: InitStatusReport = {
           ...statusReportBase,
           tools_input: "",
+          effective_tools_input: "",
+          effective_tools_input_source: EffectiveToolsInputSource.None,
+          tools_repo_property_mode: "",
           tools_resolved_version: "foo",
           tools_source: ToolsSource.Unknown,
           workflow_languages: "actions",
@@ -347,6 +351,8 @@ testCreateInitWithConfigStatusReport.serial(
     languages: [BuiltInLanguage.java, BuiltInLanguage.swift],
   }),
   {
+    effective_tools_input_source: EffectiveToolsInputSource.None,
+    tools_repo_property_mode: "",
     trap_cache_download_size_bytes: 1024,
     registries: "[]",
     query_filters: "[]",
@@ -354,6 +360,63 @@ testCreateInitWithConfigStatusReport.serial(
   },
 );
 
+test.serial(
+  "createInitWithConfigStatusReport preserves tools telemetry fields",
+  async (t) => {
+    await withTmpDir(async (tmpDir: string) => {
+      setupEnvironmentAndStub(tmpDir);
+
+      const config = createTestConfig({
+        buildMode: BuildMode.None,
+        languages: [BuiltInLanguage.java],
+      });
+
+      const statusReportBase = await createStatusReportBase(
+        ActionName.Init,
+        "failure",
+        new Date("May 19, 2023 05:19:00"),
+        config,
+        { numAvailableBytes: 100, numTotalBytes: 500 },
+        getRunnerLogger(false),
+        "failure cause",
+        "exception stack trace",
+      );
+
+      if (t.truthy(statusReportBase)) {
+        const initStatusReport: InitStatusReport = {
+          ...statusReportBase,
+          tools_input: "",
+          effective_tools_input: "toolcache",
+          effective_tools_input_source:
+            EffectiveToolsInputSource.RepositoryProperty,
+          tools_repo_property_mode: "dynamic",
+          tools_resolved_version: "foo",
+          tools_source: ToolsSource.Unknown,
+          workflow_languages: "actions",
+        };
+
+        const initWithConfigStatusReport =
+          await createInitWithConfigStatusReport(
+            config,
+            initStatusReport,
+            undefined,
+            1024,
+            undefined,
+            undefined,
+          );
+
+        if (t.truthy(initWithConfigStatusReport)) {
+          t.is(
+            initWithConfigStatusReport.effective_tools_input_source,
+            EffectiveToolsInputSource.RepositoryProperty,
+          );
+          t.is(initWithConfigStatusReport.tools_repo_property_mode, "dynamic");
+        }
+      }
+    });
+  },
+);
+
 testCreateInitWithConfigStatusReport.serial(
   "includes packs for a single language",
   createTestConfig({
diff --git a/src/status-report.ts b/src/status-report.ts
index b3e3628b36..c3165d96fc 100644
--- a/src/status-report.ts
+++ b/src/status-report.ts
@@ -12,6 +12,7 @@ import {
   isSelfHostedRunner,
 } from "./actions-util";
 import { getAnalysisKey, getApiClient } from "./api-client";
+import { EffectiveToolsInputSource } from "./config/resolve-tools-input";
 import { parseRegistriesWithoutCredentials, type Config } from "./config-utils";
 import { DependencyCacheRestoreStatusReport } from "./dependency-caching";
 import { DocUrl } from "./doc-url";
@@ -482,6 +483,12 @@ export async function sendStatusReport<S extends StatusReportBase>(
 export interface InitStatusReport extends StatusReportBase {
   /** Value given by the user as the "tools" input. */
   tools_input: string;
+  /** The effective tools input that was used, after applying defaults and repository properties. */
+  effective_tools_input: string;
+  /** Indicates where the effective tools input was resolved from. */
+  effective_tools_input_source: EffectiveToolsInputSource;
+  /** The value of the tools repository property mode, if relevant. */
+  tools_repo_property_mode: string;
   /** Version of the bundle used. */
   tools_resolved_version: string;
   /** Where the bundle originated from. */
diff --git a/src/tracer-config.test.ts b/src/tracer-config.test.ts
index 58f844b8e7..b28749cfb2 100644
--- a/src/tracer-config.test.ts
+++ b/src/tracer-config.test.ts
@@ -6,7 +6,7 @@ import * as sinon from "sinon";
 
 import { CodeQL, getCodeQLForTesting } from "./codeql";
 import * as configUtils from "./config-utils";
-import { BuiltInLanguage } from "./languages";
+import { BuiltInLanguage } from "./languages/index";
 import { createTestConfig, makeVersionInfo, setupTests } from "./testing-utils";
 import { ToolsFeature } from "./tools-features";
 import { getCombinedTracerConfig } from "./tracer-config";
diff --git a/src/trap-caching.test.ts b/src/trap-caching.test.ts
index 9805475796..bc819721ef 100644
--- a/src/trap-caching.test.ts
+++ b/src/trap-caching.test.ts
@@ -15,7 +15,7 @@ import {
 import * as configUtils from "./config-utils";
 import { Feature } from "./feature-flags";
 import * as gitUtils from "./git-utils";
-import { BuiltInLanguage } from "./languages";
+import { BuiltInLanguage } from "./languages/index";
 import { getRunnerLogger } from "./logging";
 import {
   createFeatures,
diff --git a/src/trap-caching.ts b/src/trap-caching.ts
index 216122d47e..c105f201d1 100644
--- a/src/trap-caching.ts
+++ b/src/trap-caching.ts
@@ -10,7 +10,7 @@ import { type Config } from "./config-utils";
 import { DocUrl } from "./doc-url";
 import { Feature, FeatureEnablement } from "./feature-flags";
 import * as gitUtils from "./git-utils";
-import { Language } from "./languages";
+import { Language } from "./languages/index";
 import { Logger } from "./logging";
 import {
   asHTTPError,
diff --git a/src/util.ts b/src/util.ts
index e2331461bd..2e053457da 100644
--- a/src/util.ts
+++ b/src/util.ts
@@ -15,7 +15,7 @@ import type { Pack } from "./config/db-config";
 import type { Config } from "./config-utils";
 import { EnvVar } from "./environment";
 import * as json from "./json";
-import { Language } from "./languages";
+import { Language } from "./languages/index";
 import { Logger } from "./logging";
 
 /**