diff --git a/lib/entry-points.js b/lib/entry-points.js
index 93a4d0ed58..cdbd6ab82b 100644
--- a/lib/entry-points.js
+++ b/lib/entry-points.js
@@ -145942,6 +145942,11 @@ var featureConfig = {
     envVar: "CODEQL_ACTION_CLEANUP_TRAP_CACHES",
     minimumVersion: void 0
   },
+  ["config_file_repository_property" /* ConfigFileRepositoryProperty */]: {
+    defaultValue: false,
+    envVar: "CODEQL_ACTION_CONFIG_FILE_REPOSITORY_PROPERTY",
+    minimumVersion: void 0
+  },
   ["cpp_dependency_installation_enabled" /* CppDependencyInstallation */]: {
     defaultValue: false,
     envVar: "CODEQL_EXTRACTOR_CPP_AUTOINSTALL_DEPENDENCIES",
@@ -159647,7 +159652,7 @@ var io7 = __toESM(require_io());
 var semver10 = __toESM(require_semver2());
 
 // src/config/file.ts
-function getConfigFileInput(logger, actions, repositoryProperties) {
+function getConfigFileInput(logger, actions, repositoryProperties, useRepositoryProperty) {
   const input = actions.getOptionalInput("config-file");
   if (input !== void 0) {
     logger.info(`Using configuration file input from workflow: ${input}`);
@@ -159655,10 +159660,16 @@ function getConfigFileInput(logger, actions, repositoryProperties) {
   }
   const propertyValue = repositoryProperties["github-codeql-config-file" /* CONFIG_FILE */];
   if (propertyValue !== void 0 && propertyValue.trim().length > 0) {
-    logger.info(
-      `Using configuration file input from repository property: ${propertyValue}`
-    );
-    return propertyValue;
+    if (useRepositoryProperty) {
+      logger.info(
+        `Using configuration file input from repository property: ${propertyValue}`
+      );
+      return propertyValue;
+    } else {
+      logger.info(
+        "Ignoring configuration file input from repository property, because the corresponding feature flag is disabled."
+      );
+    }
   }
   return void 0;
 }
@@ -160043,7 +160054,15 @@ async function run3(startedAt) {
     logger.info(`Job run UUID is ${jobRunUuid}.`);
     core20.exportVariable("JOB_RUN_UUID" /* JOB_RUN_UUID */, jobRunUuid);
     core20.exportVariable("CODEQL_ACTION_INIT_HAS_RUN" /* INIT_ACTION_HAS_RUN */, "true");
-    configFile = getConfigFileInput(logger, actionsEnv, repositoryProperties);
+    const useConfigFileProperty = await features.getValue(
+      "config_file_repository_property" /* ConfigFileRepositoryProperty */
+    );
+    configFile = getConfigFileInput(
+      logger,
+      actionsEnv,
+      repositoryProperties,
+      useConfigFileProperty
+    );
     sourceRoot = path24.resolve(
       getRequiredEnvParam("GITHUB_WORKSPACE"),
       getOptionalInput("source-root") || ""
diff --git a/src/config/file.test.ts b/src/config/file.test.ts
index 4c511c1a70..fef6088297 100644
--- a/src/config/file.test.ts
+++ b/src/config/file.test.ts
@@ -15,7 +15,7 @@ setupTests(test);
 test("getConfigFileInput returns undefined by default", async (t) => {
   const logger = new RecordingLogger();
   const actionsEnv = getTestActionsEnv();
-  const result = getConfigFileInput(logger, actionsEnv, {});
+  const result = getConfigFileInput(logger, actionsEnv, {}, true);
   t.is(result, undefined);
 });
 
@@ -34,7 +34,12 @@ test("getConfigFileInput returns input value", async (t) => {
 
   // Even though both an input and repository property are configured,
   // we prefer the direct input to the Action.
-  const result = getConfigFileInput(logger, actionsEnv, repositoryProperties);
+  const result = getConfigFileInput(
+    logger,
+    actionsEnv,
+    repositoryProperties,
+    true,
+  );
   t.is(result, testInput);
 
   // Check for the expected log message.
@@ -46,7 +51,12 @@ test("getConfigFileInput returns repository property value", async (t) => {
   const actionsEnv = getTestActionsEnv();
 
   // Since there is no direct input, we should use the repository property.
-  const result = getConfigFileInput(logger, actionsEnv, repositoryProperties);
+  const result = getConfigFileInput(
+    logger,
+    actionsEnv,
+    repositoryProperties,
+    true,
+  );
   t.is(result, repositoryProperties[RepositoryPropertyName.CONFIG_FILE]);
 
   // Check for the expected log message.
@@ -62,8 +72,38 @@ test("getConfigFileInput ignores empty repository property value", async (t) =>
   const actionsEnv = getTestActionsEnv();
 
   // Since the repository property value is an empty/whitespace string, we should ignore it.
-  const result = getConfigFileInput(logger, actionsEnv, {
-    [RepositoryPropertyName.CONFIG_FILE]: "   ",
-  });
+  const result = getConfigFileInput(
+    logger,
+    actionsEnv,
+    {
+      [RepositoryPropertyName.CONFIG_FILE]: "   ",
+    },
+    true,
+  );
+  t.is(result, undefined);
+});
+
+test("getConfigFileInput ignores repository property value when FF is off", async (t) => {
+  const logger = new RecordingLogger();
+  const actionsEnv = getTestActionsEnv();
+
+  // Since the FF is off, we should ignore the repository property value.
+  const result = getConfigFileInput(
+    logger,
+    actionsEnv,
+    repositoryProperties,
+    false,
+  );
   t.is(result, undefined);
+
+  t.false(
+    logger.hasMessage(
+      "Using configuration file input from repository property",
+    ),
+  );
+  t.true(
+    logger.hasMessage(
+      "Ignoring configuration file input from repository property, because the corresponding feature flag is disabled.",
+    ),
+  );
 });
diff --git a/src/config/file.ts b/src/config/file.ts
index 24613dc557..6b8dfdcdcb 100644
--- a/src/config/file.ts
+++ b/src/config/file.ts
@@ -12,6 +12,7 @@ export function getConfigFileInput(
   logger: Logger,
   actions: ActionsEnv,
   repositoryProperties: Partial<RepositoryProperties>,
+  useRepositoryProperty: boolean,
 ): string | undefined {
   const input = actions.getOptionalInput("config-file");
 
@@ -24,10 +25,17 @@ export function getConfigFileInput(
     repositoryProperties[RepositoryPropertyName.CONFIG_FILE];
 
   if (propertyValue !== undefined && propertyValue.trim().length > 0) {
-    logger.info(
-      `Using configuration file input from repository property: ${propertyValue}`,
-    );
-    return propertyValue;
+    // Only use the repository property value if the FF is enabled.
+    if (useRepositoryProperty) {
+      logger.info(
+        `Using configuration file input from repository property: ${propertyValue}`,
+      );
+      return propertyValue;
+    } else {
+      logger.info(
+        "Ignoring configuration file input from repository property, because the corresponding feature flag is disabled.",
+      );
+    }
   }
 
   return undefined;
diff --git a/src/feature-flags.ts b/src/feature-flags.ts
index a796982242..f71ecab57b 100644
--- a/src/feature-flags.ts
+++ b/src/feature-flags.ts
@@ -74,6 +74,8 @@ export enum Feature {
   AllowMultipleAnalysisKinds = "allow_multiple_analysis_kinds",
   AllowToolcacheInput = "allow_toolcache_input",
   CleanupTrapCaches = "cleanup_trap_caches",
+  /** Whether to allow the `config-file` input to be specified via a repository property. */
+  ConfigFileRepositoryProperty = "config_file_repository_property",
   CppDependencyInstallation = "cpp_dependency_installation_enabled",
   CsharpCacheBuildModeNone = "csharp_cache_bmn",
   CsharpNewCacheKey = "csharp_new_cache_key",
@@ -184,6 +186,11 @@ export const featureConfig = {
     envVar: "CODEQL_ACTION_CLEANUP_TRAP_CACHES",
     minimumVersion: undefined,
   },
+  [Feature.ConfigFileRepositoryProperty]: {
+    defaultValue: false,
+    envVar: "CODEQL_ACTION_CONFIG_FILE_REPOSITORY_PROPERTY",
+    minimumVersion: undefined,
+  },
   [Feature.CppDependencyInstallation]: {
     defaultValue: false,
     envVar: "CODEQL_EXTRACTOR_CPP_AUTOINSTALL_DEPENDENCIES",
diff --git a/src/init-action.ts b/src/init-action.ts
index 9c9b45556b..ec711cdf0b 100644
--- a/src/init-action.ts
+++ b/src/init-action.ts
@@ -263,7 +263,15 @@ async function run(startedAt: Date) {
 
     core.exportVariable(EnvVar.INIT_ACTION_HAS_RUN, "true");
 
-    configFile = getConfigFileInput(logger, actionsEnv, repositoryProperties);
+    const useConfigFileProperty = await features.getValue(
+      Feature.ConfigFileRepositoryProperty,
+    );
+    configFile = getConfigFileInput(
+      logger,
+      actionsEnv,
+      repositoryProperties,
+      useConfigFileProperty,
+    );
 
     // path.resolve() respects the intended semantics of source-root. If
     // source-root is relative, it is relative to the GITHUB_WORKSPACE. If