diff --git a/src/codeql.ts b/src/codeql.ts
index 9dea038d8..540a2b849 100644
--- a/src/codeql.ts
+++ b/src/codeql.ts
@@ -1274,6 +1274,15 @@ async function generateCodeScanningConfig(
   if (Array.isArray(augmentedConfig.packs) && !augmentedConfig.packs.length) {
     delete augmentedConfig.packs;
   }
+
+  augmentedConfig["query-filters"] = [
+    ...(config.augmentationProperties.defaultQueryFilters || []),
+    ...(augmentedConfig["query-filters"] || []),
+  ];
+  if (augmentedConfig["query-filters"]?.length === 0) {
+    delete augmentedConfig["query-filters"];
+  }
+
   logger.info(
     `Writing augmented user configuration file to ${codeScanningConfigFile}`,
   );
diff --git a/src/config-utils.test.ts b/src/config-utils.test.ts
index cc8c6e928..642c833c2 100644
--- a/src/config-utils.test.ts
+++ b/src/config-utils.test.ts
@@ -809,11 +809,12 @@ const calculateAugmentationMacro = test.macro({
     languages: Language[],
     expectedAugmentationProperties: configUtils.AugmentationProperties,
   ) => {
-    const actualAugmentationProperties = configUtils.calculateAugmentation(
-      rawPacksInput,
-      rawQueriesInput,
-      languages,
-    );
+    const actualAugmentationProperties =
+      await configUtils.calculateAugmentation(
+        rawPacksInput,
+        rawQueriesInput,
+        languages,
+      );
     t.deepEqual(actualAugmentationProperties, expectedAugmentationProperties);
   },
   title: (_, title) => `Calculate Augmentation: ${title}`,
@@ -830,6 +831,7 @@ test(
     queriesInput: undefined,
     packsInputCombines: false,
     packsInput: undefined,
+    defaultQueryFilters: [],
   } as configUtils.AugmentationProperties,
 );
 
@@ -844,6 +846,7 @@ test(
     queriesInput: [{ uses: "a" }, { uses: "b" }, { uses: "c" }, { uses: "d" }],
     packsInputCombines: false,
     packsInput: undefined,
+    defaultQueryFilters: [],
   } as configUtils.AugmentationProperties,
 );
 
@@ -858,6 +861,7 @@ test(
     queriesInput: [{ uses: "a" }, { uses: "b" }, { uses: "c" }, { uses: "d" }],
     packsInputCombines: false,
     packsInput: undefined,
+    defaultQueryFilters: [],
   } as configUtils.AugmentationProperties,
 );
 
@@ -872,6 +876,7 @@ test(
     queriesInput: undefined,
     packsInputCombines: false,
     packsInput: ["codeql/a", "codeql/b", "codeql/c", "codeql/d"],
+    defaultQueryFilters: [],
   } as configUtils.AugmentationProperties,
 );
 
@@ -886,6 +891,7 @@ test(
     queriesInput: undefined,
     packsInputCombines: true,
     packsInput: ["codeql/a", "codeql/b", "codeql/c", "codeql/d"],
+    defaultQueryFilters: [],
   } as configUtils.AugmentationProperties,
 );
 
@@ -898,7 +904,7 @@ const calculateAugmentationErrorMacro = test.macro({
     languages: Language[],
     expectedError: RegExp | string,
   ) => {
-    t.throws(
+    await t.throwsAsync(
       () =>
         configUtils.calculateAugmentation(
           rawPacksInput,
diff --git a/src/config-utils.ts b/src/config-utils.ts
index 36e55ad35..008a027c0 100644
--- a/src/config-utils.ts
+++ b/src/config-utils.ts
@@ -173,10 +173,16 @@ export interface AugmentationProperties {
    * Whether or not the packs input combines with the packs in the config.
    */
   packsInputCombines: boolean;
+
   /**
    * The packs input from the `with` block of the action declaration
    */
   packsInput?: string[];
+
+  /**
+   * Default query filters to apply to the queries in the config.
+   */
+  defaultQueryFilters?: QueryFilter[];
 }
 
 /**
@@ -188,6 +194,7 @@ export const defaultAugmentationProperties: AugmentationProperties = {
   packsInputCombines: false,
   packsInput: undefined,
   queriesInput: undefined,
+  defaultQueryFilters: [],
 };
 export type Packs = Partial<Record<Language, string[]>>;
 
@@ -461,7 +468,7 @@ export async function getDefaultConfig({
     logger,
   );
 
-  const augmentationProperties = calculateAugmentation(
+  const augmentationProperties = await calculateAugmentation(
     packsInput,
     queriesInput,
     languages,
@@ -567,7 +574,7 @@ async function loadConfig({
     logger,
   );
 
-  const augmentationProperties = calculateAugmentation(
+  const augmentationProperties = await calculateAugmentation(
     packsInput,
     queriesInput,
     languages,
@@ -617,11 +624,11 @@ async function loadConfig({
  *     not have exactly one language.
  */
 // exported for testing.
-export function calculateAugmentation(
+export async function calculateAugmentation(
   rawPacksInput: string | undefined,
   rawQueriesInput: string | undefined,
   languages: Language[],
-): AugmentationProperties {
+): Promise<AugmentationProperties> {
   const packsInputCombines = shouldCombine(rawPacksInput);
   const packsInput = parsePacksFromInput(
     rawPacksInput,
@@ -634,11 +641,14 @@ export function calculateAugmentation(
     queriesInputCombines,
   );
 
+  const defaultQueryFilters: QueryFilter[] = [];
+
   return {
     packsInputCombines,
     packsInput: packsInput?.[languages[0]],
     queriesInput,
     queriesInputCombines,
+    defaultQueryFilters,
   };
 }