diff --git a/reposerver/repository/repository.go b/reposerver/repository/repository.go
index 1abccf6bcd2dd..059cf82227cb9 100644
--- a/reposerver/repository/repository.go
+++ b/reposerver/repository/repository.go
@@ -165,6 +165,7 @@ func (s *Service) Init() error {
 		fullPath := filepath.Join(s.rootDir, file.Name())
 		closer := s.gitRepoInitializer(fullPath)
 		if repo, err := gogit.PlainOpen(fullPath); err == nil {
+			s.cleanupStaleFiles(fullPath, []string{"index.lock", "index", "HEAD.lock"}, repo)
 			if remotes, err := repo.Remotes(); err == nil && len(remotes) > 0 && len(remotes[0].Config().URLs) > 0 {
 				s.gitRepoPaths.Add(git.NormalizeGitURL(remotes[0].Config().URLs[0]), fullPath)
 			}
@@ -175,6 +176,39 @@ func (s *Service) Init() error {
 	return os.Chmod(s.rootDir, 0o300)
 }
 
+func (s *Service) cleanupStaleFiles(fullPath string, staleFiles []string, repo *gogit.Repository) {
+	// for each stale file, if it exists, remove it
+	for _, staleFile := range staleFiles {
+		gitFile := filepath.Join(fullPath, ".git", staleFile)
+		info, err := os.Lstat(gitFile)
+		if err == nil {
+			// Only delete if it's a regular file (not a symlink, dir, etc.)
+			if info.Mode().IsRegular() {
+				log.Warnf("Stale file %s present in git repository %s, removing it", staleFile, fullPath)
+				if err = os.Remove(gitFile); err != nil {
+					log.Errorf("Failed to remove stale file %s: %v", gitFile, err)
+				}
+				if staleFile == "index" {
+					if err == nil {
+						wt, _ := repo.Worktree()
+						headRef, _ := repo.Head()
+						err = wt.Reset(&gogit.ResetOptions{
+							Mode:   gogit.MixedReset,
+							Commit: headRef.Hash(),
+						})
+					}
+
+					if err != nil {
+						log.Errorf("Failed to reset git repo %s: %v", fullPath, err)
+					}
+				}
+			}
+		} else {
+			log.Warnf("Stale file %s in git repository %s is not a regular file, skipping removal", staleFile, fullPath)
+		}
+	}
+}
+
 // ListRefs List a subset of the refs (currently, branches and tags) of a git repo
 func (s *Service) ListRefs(_ context.Context, q *apiclient.ListRefsRequest) (*apiclient.Refs, error) {
 	gitClient, err := s.newClient(q.Repo)
diff --git a/reposerver/repository/repository_test.go b/reposerver/repository/repository_test.go
index e96fc3540a95e..0402414a289bf 100644
--- a/reposerver/repository/repository_test.go
+++ b/reposerver/repository/repository_test.go
@@ -3014,6 +3014,53 @@ func TestInit(t *testing.T) {
 	_, err := os.ReadDir(dir)
 	require.Error(t, err)
 	initGitRepo(t, newGitRepoOptions{path: path.Join(dir, "repo2"), remote: "https://github.com/argo-cd/test-repo2", createPath: true, addEmptyCommit: false})
+
+	repoPath = path.Join(dir, "repo3")
+	indexLockFile := path.Join(repoPath, ".git", "index.lock")
+	indexFile := path.Join(repoPath, ".git", "index")
+	headLockFile := path.Join(repoPath, ".git", "HEAD.lock")
+	initGitRepo(t, newGitRepoOptions{path: repoPath, remote: "https://github.com/argo-cd/test-repo3", createPath: true, addEmptyCommit: true})
+	require.NoError(t, os.WriteFile(indexLockFile, []byte("test"), 0o644))
+	require.NoError(t, os.WriteFile(headLockFile, []byte("test"), 0o644))
+
+	service = newService(t, ".")
+	service.rootDir = dir
+
+	_, err = os.Stat(indexLockFile)
+	require.NoError(t, err)
+	_, err = os.Stat(indexFile)
+	require.NoError(t, err)
+	_, err = os.Stat(headLockFile)
+	require.NoError(t, err)
+
+	require.NoError(t, service.Init())
+
+	_, err = os.Stat(indexLockFile)
+	require.Error(t, err, "index.lock file should be removed after Init()")
+	require.ErrorContains(t, err, ".git/index.lock: no such file or directory")
+	_, err = os.Stat(indexFile)
+	// index file should stay after Init(), since it was recreated after repo reset
+	require.NoError(t, err)
+	_, err = os.Stat(headLockFile)
+	require.Error(t, err, "HEAD.lock file should be removed after Init()")
+	require.ErrorContains(t, err, ".git/HEAD.lock: no such file or directory")
+
+	repoPath = path.Join(dir, "repo4")
+	headLockDir := path.Join(repoPath, ".git", "HEAD.lock")
+	initGitRepo(t, newGitRepoOptions{path: repoPath, remote: "https://github.com/argo-cd/test-repo4", createPath: true, addEmptyCommit: false})
+	require.NoError(t, os.Mkdir(headLockDir, 0o755))
+
+	service = newService(t, ".")
+	service.rootDir = dir
+
+	_, err = os.Stat(headLockDir)
+	require.NoError(t, err)
+
+	require.NoError(t, service.Init())
+
+	_, err = os.Stat(headLockDir)
+	// headLockDir should stay after Init(), since it is a directory
+	require.NoError(t, err)
 }
 
 // TestCheckoutRevisionCanGetNonstandardRefs shows that we can fetch a revision that points to a non-standard ref. In