diff --git a/lib/util/git/index.spec.ts b/lib/util/git/index.spec.ts
index be08b2763b2..e8792ade287 100644
--- a/lib/util/git/index.spec.ts
+++ b/lib/util/git/index.spec.ts
@@ -1046,6 +1046,26 @@ describe('util/git/index', { timeout: 10000 }, () => {
       const res = (await repo.raw(['config', 'extra.clone.config'])).trim();
       expect(res).toBe('test-extra-config-value');
     });
+
+    it('should not pass extraCloneOpts to ls-remote when local repo exists', async () => {
+      const extraCloneOpts = {
+        '-c': 'extra.clone.config=test-extra-config-value',
+      };
+
+      await fs.emptyDir(tmpDir.path);
+      await git.initRepo({ url: origin.path, extraCloneOpts, fullClone: true });
+      await git.syncGit();
+
+      const rawSpy = vi.spyOn(SimpleGit.prototype, 'raw');
+
+      await git.initRepo({ url: origin.path, extraCloneOpts, fullClone: true });
+
+      expect(rawSpy).toHaveBeenCalledWith([
+        'ls-remote',
+        '--heads',
+        origin.path,
+      ]);
+    });
   });
 
   describe('setGitAuthor()', () => {
diff --git a/lib/util/git/index.ts b/lib/util/git/index.ts
index 982c404eec1..81ae7ce34e7 100644
--- a/lib/util/git/index.ts
+++ b/lib/util/git/index.ts
@@ -208,7 +208,9 @@ async function fetchBranchCommits(preferUpstream = true): Promise<void> {
     preferUpstream && config.upstreamUrl ? config.upstreamUrl : config.url;
   logger.debug(`fetchBranchCommits(): url=${url}`);
   const opts = ['ls-remote', '--heads', url];
-  if (config.extraCloneOpts) {
+  const localDir = GlobalConfig.get('localDir')!;
+  const repoExists = await fs.pathExists(upath.join(localDir, '.git/HEAD'));
+  if (config.extraCloneOpts && !repoExists) {
     Object.entries(config.extraCloneOpts).forEach((e) =>
       // TODO: types (#22198)
       opts.unshift(e[0], `${e[1]!}`),