diff --git a/lib/init-action.js b/lib/init-action.js
index a5fcd7687..bf8138277 100644
--- a/lib/init-action.js
+++ b/lib/init-action.js
@@ -87616,6 +87616,15 @@ async function initActionState({
     repositoryProperties,
     languages
   );
+  if (analysisKinds.length === 1 && analysisKinds.includes("code-quality" /* CodeQuality */) && augmentationProperties.repoPropertyQueries.input) {
+    logger.info(
+      `Ignoring queries configured in the repository properties, because query customisations are not supported for Code Quality analyses.`
+    );
+    augmentationProperties.repoPropertyQueries = {
+      combines: false,
+      input: void 0
+    };
+  }
   const { trapCaches, trapCacheDownloadTime } = await downloadCacheWithTime(
     trapCachingEnabled,
     codeql,
diff --git a/src/config-utils.test.ts b/src/config-utils.test.ts
index 1df142f11..566a719ca 100644
--- a/src/config-utils.test.ts
+++ b/src/config-utils.test.ts
@@ -29,6 +29,7 @@ import {
   getRecordingLogger,
   LoggedMessage,
   mockCodeQLVersion,
+  createTestConfig,
 } from "./testing-utils";
 import {
   GitHubVariant,
@@ -230,6 +231,63 @@ test("load code quality config", async (t) => {
   });
 });
 
+test("initActionState doesn't throw if there are queries configured in the repository properties", async (t) => {
+  return await withTmpDir(async (tempDir) => {
+    const logger = getRunnerLogger(true);
+    const languages = "javascript";
+
+    const codeql = createStubCodeQL({
+      async betterResolveLanguages() {
+        return {
+          extractors: {
+            javascript: [{ extractor_root: "" }],
+          },
+        };
+      },
+    });
+
+    // This should be ignored and no error should be thrown.
+    const repositoryProperties = {
+      "github-codeql-extra-queries": "+foo",
+    };
+
+    // Expected configuration for a CQ-only analysis.
+    const computedConfig: configUtils.UserConfig = {
+      "disable-default-queries": true,
+      queries: [{ uses: "code-quality" }],
+      "query-filters": [],
+    };
+
+    const expectedConfig = createTestConfig({
+      analysisKinds: [AnalysisKind.CodeQuality],
+      languages: [KnownLanguage.javascript],
+      codeQLCmd: codeql.getPath(),
+      computedConfig,
+      dbLocation: path.resolve(tempDir, "codeql_databases"),
+      debugArtifactName: "",
+      debugDatabaseName: "",
+      tempDir,
+      repositoryProperties,
+    });
+
+    await t.notThrowsAsync(async () => {
+      const config = await configUtils.initConfig(
+        createTestInitConfigInputs({
+          analysisKindsInput: "code-quality",
+          languagesInput: languages,
+          repository: { owner: "github", repo: "example" },
+          tempDir,
+          codeql,
+          repositoryProperties,
+          logger,
+        }),
+      );
+
+      t.deepEqual(config, expectedConfig);
+    });
+  });
+});
+
 test("loading a saved config produces the same config", async (t) => {
   return await withTmpDir(async (tempDir) => {
     const logger = getRunnerLogger(true);
diff --git a/src/config-utils.ts b/src/config-utils.ts
index e6e99be3b..fe4b392ab 100644
--- a/src/config-utils.ts
+++ b/src/config-utils.ts
@@ -463,6 +463,24 @@ export async function initActionState(
     languages,
   );
 
+  // If `code-quality` is the only enabled analysis kind, we don't support query customisation.
+  // It would be a problem if queries that are configured in repository properties cause `code-quality`-only
+  // analyses to break. We therefore ignore query customisations that are configured in repository properties
+  // if `code-quality` is the only enabled analysis kind.
+  if (
+    analysisKinds.length === 1 &&
+    analysisKinds.includes(AnalysisKind.CodeQuality) &&
+    augmentationProperties.repoPropertyQueries.input
+  ) {
+    logger.info(
+      `Ignoring queries configured in the repository properties, because query customisations are not supported for Code Quality analyses.`,
+    );
+    augmentationProperties.repoPropertyQueries = {
+      combines: false,
+      input: undefined,
+    };
+  }
+
   const { trapCaches, trapCacheDownloadTime } = await downloadCacheWithTime(
     trapCachingEnabled,
     codeql,