diff --git a/lib/entry-points.js b/lib/entry-points.js
index 528f258a87..46c44a8183 100644
--- a/lib/entry-points.js
+++ b/lib/entry-points.js
@@ -148495,22 +148495,27 @@ async function getConfigFileInput({
   logger,
   actions,
   features
-}, repositoryProperties) {
+}, repositoryProperties, analysisKinds) {
   const input = actions.getOptionalInput("config-file");
   if (input !== void 0) {
     logger.info(`Using configuration file input from workflow: ${input}`);
     return input;
   }
   const propertyValue = repositoryProperties["github-codeql-config-file" /* CONFIG_FILE */];
+  const analysisKindSupported = analysisKinds === void 0 || analysisKinds.includes("code-scanning" /* CodeScanning */) && analysisKinds.length === 1;
   if (propertyValue !== void 0 && propertyValue.trim().length > 0) {
     const useRepositoryProperty = await features.getValue(
       "config_file_repository_property" /* ConfigFileRepositoryProperty */
     );
-    if (useRepositoryProperty) {
+    if (analysisKindSupported && useRepositoryProperty) {
       logger.info(
         `Using configuration file input from repository property: ${propertyValue}`
       );
       return propertyValue;
+    } else if (!analysisKindSupported) {
+      logger.info(
+        "Ignoring configuration file input from repository property, because it is unsupported for the current analysis kind."
+      );
     } else {
       logger.info(
         "Ignoring configuration file input from repository property, because the corresponding feature flag is disabled."
@@ -160750,11 +160755,6 @@ async function run3(actionState) {
     logger.info(`Job run UUID is ${jobRunUuid}.`);
     core21.exportVariable("JOB_RUN_UUID" /* JOB_RUN_UUID */, jobRunUuid);
     core21.exportVariable("CODEQL_ACTION_INIT_HAS_RUN" /* INIT_ACTION_HAS_RUN */, "true");
-    const actionStateWithFeatures = { ...actionState, features };
-    configFile = await getConfigFileInput(
-      actionStateWithFeatures,
-      repositoryProperties
-    );
     sourceRoot = path24.resolve(
       getRequiredEnvParam("GITHUB_WORKSPACE"),
       getOptionalInput("source-root") || ""
@@ -160767,6 +160767,12 @@ async function run3(actionState) {
         `Failed to parse analysis kinds for 'starting' status report: ${getErrorMessage(err)}`
       );
     }
+    const actionStateWithFeatures = { ...actionState, features };
+    configFile = await getConfigFileInput(
+      actionStateWithFeatures,
+      repositoryProperties,
+      analysisKinds
+    );
     await sendStartingStatusReport(startedAt, { analysisKinds }, logger);
     if (process.env["CODEQL_ACTION_SETUP_CODEQL_HAS_RUN" /* SETUP_CODEQL_ACTION_HAS_RUN */] === "true") {
       throw new ConfigurationError(
diff --git a/src/config/file.test.ts b/src/config/file.test.ts
index 22e2f795f8..0833ad3d06 100644
--- a/src/config/file.test.ts
+++ b/src/config/file.test.ts
@@ -2,6 +2,7 @@ import * as github from "@actions/github";
 import test from "ava";
 import sinon from "sinon";
 
+import { AnalysisKind } from "../analyses";
 import * as api from "../api-client";
 import { RegistryProxyVars } from "../environment";
 import { Feature } from "../feature-flags";
@@ -18,7 +19,7 @@ setupTests(test);
 
 test("getConfigFileInput returns undefined by default", async (t) => {
   await callee(getConfigFileInput)
-    .withArgs({})
+    .withArgs({}, undefined)
     .withFeatures([Feature.ConfigFileRepositoryProperty])
     .passes(t.is, undefined);
 });
@@ -40,7 +41,7 @@ test("getConfigFileInput returns input value", async (t) => {
         .withArgs("config-file")
         .returns(testInput);
     })
-    .withArgs(repositoryProperties)
+    .withArgs(repositoryProperties, undefined)
     .logs(t, "Using configuration file input from workflow")
     .passes(t.is, testInput);
 });
@@ -49,16 +50,48 @@ test("getConfigFileInput returns repository property value", async (t) => {
   // Since there is no direct input, we should use the repository property.
   await callee(getConfigFileInput)
     .withFeatures([Feature.ConfigFileRepositoryProperty])
-    .withArgs(repositoryProperties)
+    .withArgs(repositoryProperties, undefined)
     .logs(t, "Using configuration file input from repository property")
     .passes(t.is, repositoryProperties[RepositoryPropertyName.CONFIG_FILE]);
 });
 
+test("getConfigFileInput returns repository property value for Code Scanning", async (t) => {
+  // Since there is no direct input, we should use the repository property.
+  await callee(getConfigFileInput)
+    .withFeatures([Feature.ConfigFileRepositoryProperty])
+    .withArgs(repositoryProperties, [AnalysisKind.CodeScanning])
+    .logs(t, "Using configuration file input from repository property")
+    .passes(t.is, repositoryProperties[RepositoryPropertyName.CONFIG_FILE]);
+});
+
+test("getConfigFileInput ignores repository property for other analysis kinds", async (t) => {
+  const unsupportedCases = [
+    [AnalysisKind.CodeQuality],
+    [AnalysisKind.RiskAssessment],
+    [AnalysisKind.CodeScanning, AnalysisKind.CodeQuality],
+  ];
+
+  const target = callee(getConfigFileInput).withFeatures([
+    Feature.ConfigFileRepositoryProperty,
+  ]);
+
+  for (const unsupportedCase of unsupportedCases) {
+    // Since the analysis kind is unsupported, we should ignore the repository property.
+    await target
+      .withArgs(repositoryProperties, unsupportedCase)
+      .logs(
+        t,
+        "Ignoring configuration file input from repository property, because it is unsupported for the current analysis kind.",
+      )
+      .passes(t.is, undefined);
+  }
+});
+
 test("getConfigFileInput ignores empty repository property value", async (t) => {
   // Since the repository property value is an empty/whitespace string, we should ignore it.
   await callee(getConfigFileInput)
     .withFeatures([Feature.ConfigFileRepositoryProperty])
-    .withArgs({ [RepositoryPropertyName.CONFIG_FILE]: "   " })
+    .withArgs({ [RepositoryPropertyName.CONFIG_FILE]: "   " }, undefined)
     .passes(t.is, undefined);
 });
 
@@ -66,7 +99,7 @@ test("getConfigFileInput ignores repository property value when FF is off", asyn
   // Since the FF is off, we should ignore the repository property value.
   await callee(getConfigFileInput)
     .withFeatures([])
-    .withArgs(repositoryProperties)
+    .withArgs(repositoryProperties, undefined)
     .notLogs(t, "Using configuration file input from repository property")
     .logs(
       t,
diff --git a/src/config/file.ts b/src/config/file.ts
index 8cb7bc3a11..be0e415a38 100644
--- a/src/config/file.ts
+++ b/src/config/file.ts
@@ -1,4 +1,5 @@
 import { ActionState } from "../action-common";
+import { AnalysisKind } from "../analyses";
 import * as api from "../api-client";
 import * as errorMessages from "../error-messages";
 import { Feature } from "../feature-flags";
@@ -34,6 +35,7 @@ export async function getConfigFileInput(
     features,
   }: ActionState<["Logger", "Actions", "FeatureFlags"]>,
   repositoryProperties: Partial<RepositoryProperties>,
+  analysisKinds: AnalysisKind[] | undefined,
 ): Promise<string | undefined> {
   const input = actions.getOptionalInput("config-file");
 
@@ -45,17 +47,29 @@ export async function getConfigFileInput(
   const propertyValue =
     repositoryProperties[RepositoryPropertyName.CONFIG_FILE];
 
+  // Only allow the repository property to be used for standard Code Scanning analyses,
+  // since we don't currently support some customisation options for Code Quality.
+  // We don't expect customisations for Risk Assessments either.
+  const analysisKindSupported =
+    analysisKinds === undefined ||
+    (analysisKinds.includes(AnalysisKind.CodeScanning) &&
+      analysisKinds.length === 1);
+
   if (propertyValue !== undefined && propertyValue.trim().length > 0) {
     // Only use the repository property value if the FF is enabled.
     const useRepositoryProperty = await features.getValue(
       Feature.ConfigFileRepositoryProperty,
     );
 
-    if (useRepositoryProperty) {
+    if (analysisKindSupported && useRepositoryProperty) {
       logger.info(
         `Using configuration file input from repository property: ${propertyValue}`,
       );
       return propertyValue;
+    } else if (!analysisKindSupported) {
+      logger.info(
+        "Ignoring configuration file input from repository property, because it is unsupported for the current analysis kind.",
+      );
     } else {
       logger.info(
         "Ignoring configuration file input from repository property, because the corresponding feature flag is disabled.",
diff --git a/src/init-action.ts b/src/init-action.ts
index c7837c6eed..4b52ba6ec6 100644
--- a/src/init-action.ts
+++ b/src/init-action.ts
@@ -262,12 +262,6 @@ async function run(
 
     core.exportVariable(EnvVar.INIT_ACTION_HAS_RUN, "true");
 
-    const actionStateWithFeatures = { ...actionState, features };
-    configFile = await getConfigFileInput(
-      actionStateWithFeatures,
-      repositoryProperties,
-    );
-
     // path.resolve() respects the intended semantics of source-root. If
     // source-root is relative, it is relative to the GITHUB_WORKSPACE. If
     // source-root is absolute, it is used as given.
@@ -290,6 +284,14 @@ async function run(
       );
     }
 
+    // Compute the value of the `config-file` input.
+    const actionStateWithFeatures = { ...actionState, features };
+    configFile = await getConfigFileInput(
+      actionStateWithFeatures,
+      repositoryProperties,
+      analysisKinds,
+    );
+
     // Send a status report indicating that an analysis is starting.
     await sendStartingStatusReport(startedAt, { analysisKinds }, logger);