diff --git a/extensions/ql-vscode/src/skeleton-query-wizard.ts b/extensions/ql-vscode/src/skeleton-query-wizard.ts
index 7449f1f7d..54a265fbe 100644
--- a/extensions/ql-vscode/src/skeleton-query-wizard.ts
+++ b/extensions/ql-vscode/src/skeleton-query-wizard.ts
@@ -185,7 +185,7 @@ export class SkeletonQueryWizard {
     const folderUri = Uri.file(join(this.storagePath, folderName));
     const files = await workspace.fs.readDirectory(folderUri);
     const qlFiles = files.filter(([filename, _fileType]) =>
-      filename.endsWith(".ql"),
+      filename.match(/example[0-9]*.ql/),
     );
 
     return `example${qlFiles.length + 1}.ql`;
diff --git a/extensions/ql-vscode/test/vscode-tests/cli-integration/skeleton-query-wizard.test.ts b/extensions/ql-vscode/test/vscode-tests/cli-integration/skeleton-query-wizard.test.ts
index c01c9a3b7..2202a3487 100644
--- a/extensions/ql-vscode/test/vscode-tests/cli-integration/skeleton-query-wizard.test.ts
+++ b/extensions/ql-vscode/test/vscode-tests/cli-integration/skeleton-query-wizard.test.ts
@@ -9,7 +9,7 @@ import { TextDocument, window, workspace, WorkspaceFolder } from "vscode";
 import { extLogger } from "../../../src/common";
 import { QlPackGenerator } from "../../../src/qlpack-generator";
 import * as helpers from "../../../src/helpers";
-import { ensureDirSync, removeSync } from "fs-extra";
+import { createFileSync, ensureDirSync, removeSync } from "fs-extra";
 import { join } from "path";
 import { CancellationTokenSource } from "vscode-jsonrpc";
 import { testCredentialsWithStub } from "../../factories/authentication";
@@ -158,6 +158,16 @@ describe("SkeletonQueryWizard", () => {
       expect(createExampleQlFileSpy).toHaveBeenCalledWith("example2.ql");
     });
 
+    it("should only take into account example QL files", async () => {
+      createFileSync(
+        join(dir.name, `codeql-custom-queries-${chosenLanguage}`, "MyQuery.ql"),
+      );
+
+      await wizard.execute();
+
+      expect(createExampleQlFileSpy).toHaveBeenCalledWith("example2.ql");
+    });
+
     describe("if QL pack has no query file", () => {
       it("should create new query file in the same QL pack folder", async () => {
         removeSync(