diff --git a/lib/init-action.js b/lib/init-action.js
index a3b4cf1f56..03b08575ba 100644
--- a/lib/init-action.js
+++ b/lib/init-action.js
@@ -86985,7 +86985,7 @@ function userConfigFromActionPath(tempDir) {
   return path7.resolve(tempDir, "user-config-from-action.yml");
 }
 function hasQueryCustomisation(userConfig) {
-  return isDefined(userConfig["disable-default-queries"]) || isDefined(userConfig.queries) || isDefined(userConfig["query-filters"]);
+  return isDefined(userConfig["disable-default-queries"]) || isDefined(userConfig.queries);
 }
 async function initConfig(features, inputs) {
   const { logger, tempDir } = inputs;
@@ -87024,7 +87024,6 @@ async function initConfig(features, inputs) {
     const queries = codeQualityQueries.map((v) => ({ uses: v }));
     config.computedConfig["disable-default-queries"] = true;
     config.computedConfig.queries = queries;
-    config.computedConfig["query-filters"] = [];
   }
   const { overlayDatabaseMode, useOverlayDatabaseCaching } = await getOverlayDatabaseMode(
     inputs.codeql,
diff --git a/src/config-utils.test.ts b/src/config-utils.test.ts
index bf60b4902e..a8ac7610d9 100644
--- a/src/config-utils.test.ts
+++ b/src/config-utils.test.ts
@@ -210,7 +210,6 @@ test("load code quality config", async (t) => {
       computedConfig: {
         "disable-default-queries": true,
         queries: [{ uses: "code-quality" }],
-        "query-filters": [],
       },
       tempDir,
       codeQLCmd: codeql.getPath(),
@@ -256,7 +255,6 @@ test("initActionState doesn't throw if there are queries configured in the repos
     const computedConfig: configUtils.UserConfig = {
       "disable-default-queries": true,
       queries: [{ uses: "code-quality" }],
-      "query-filters": [],
     };
 
     const expectedConfig = createTestConfig({
diff --git a/src/config-utils.ts b/src/config-utils.ts
index 3a1d040db0..5065a48e0d 100644
--- a/src/config-utils.ts
+++ b/src/config-utils.ts
@@ -776,8 +776,7 @@ function userConfigFromActionPath(tempDir: string): string {
 function hasQueryCustomisation(userConfig: UserConfig): boolean {
   return (
     isDefined(userConfig["disable-default-queries"]) ||
-    isDefined(userConfig.queries) ||
-    isDefined(userConfig["query-filters"])
+    isDefined(userConfig.queries)
   );
 }
 
@@ -839,7 +838,6 @@ export async function initConfig(
     // Set the query customisation options for Code Quality only analysis.
     config.computedConfig["disable-default-queries"] = true;
     config.computedConfig.queries = queries;
-    config.computedConfig["query-filters"] = [];
   }
 
   // The choice of overlay database mode depends on the selection of languages