diff --git a/cmd/bd/migrate_sync.go b/cmd/bd/migrate_sync.go
index e12b4740..e4f8af4f 100644
--- a/cmd/bd/migrate_sync.go
+++ b/cmd/bd/migrate_sync.go
@@ -155,12 +155,12 @@ func runMigrateSync(ctx context.Context, branchName string, dryRun, force bool)
 			fmt.Printf("→ Would create new branch '%s'\n", branchName)
 		}
 
-		// Use worktree-aware git directory detection
-		gitDir, err := git.GetGitDir()
+		// Use git-common-dir for worktree path to support bare repos and worktrees (GH#639)
+		gitCommonDir, err := git.GetGitCommonDir()
 		if err != nil {
 			return fmt.Errorf("not a git repository: %w", err)
 		}
-		worktreePath := filepath.Join(gitDir, "beads-worktrees", branchName)
+		worktreePath := filepath.Join(gitCommonDir, "beads-worktrees", branchName)
 		fmt.Printf("→ Would create worktree at: %s\n", worktreePath)
 
 		fmt.Println("\n=== END DRY RUN ===")
@@ -195,12 +195,12 @@ func runMigrateSync(ctx context.Context, branchName string, dryRun, force bool)
 	}
 
 	// Step 2: Create the worktree
-	// Use worktree-aware git directory detection
-	gitDir, err := git.GetGitDir()
+	// Use git-common-dir for worktree path to support bare repos and worktrees (GH#639)
+	gitCommonDir, err := git.GetGitCommonDir()
 	if err != nil {
 		return fmt.Errorf("not a git repository: %w", err)
 	}
-	worktreePath := filepath.Join(gitDir, "beads-worktrees", branchName)
+	worktreePath := filepath.Join(gitCommonDir, "beads-worktrees", branchName)
 	fmt.Printf("→ Creating worktree at %s...\n", worktreePath)
 
 	wtMgr := git.NewWorktreeManager(repoRoot)
diff --git a/internal/git/gitdir.go b/internal/git/gitdir.go
index 116fe910..dd11b531 100644
--- a/internal/git/gitdir.go
+++ b/internal/git/gitdir.go
@@ -100,6 +100,23 @@ func GetGitDir() (string, error) {
 	return ctx.gitDir, nil
 }
 
+// GetGitCommonDir returns the common git directory shared across all worktrees.
+// For regular repos, this equals GetGitDir(). For worktrees, this returns
+// the main repository's .git directory where shared data (like worktree
+// registrations, hooks, and objects) lives.
+//
+// Use this instead of GetGitDir() when you need to create new worktrees or
+// access shared git data that should not be scoped to a single worktree.
+// GH#639: This is critical for bare repo setups where GetGitDir() returns
+// a worktree-specific path that cannot host new worktrees.
+func GetGitCommonDir() (string, error) {
+	ctx, err := getGitContext()
+	if err != nil {
+		return "", err
+	}
+	return ctx.commonDir, nil
+}
+
 // GetGitHooksDir returns the path to the Git hooks directory.
 // This function is worktree-aware and handles both regular repos and worktrees.
 func GetGitHooksDir() (string, error) {
diff --git a/internal/syncbranch/worktree.go b/internal/syncbranch/worktree.go
index 379829d8..134b34c5 100644
--- a/internal/syncbranch/worktree.go
+++ b/internal/syncbranch/worktree.go
@@ -987,8 +987,9 @@ func GetRepoRoot(ctx context.Context) (string, error) {
 			line := strings.TrimSpace(string(content))
 			if strings.HasPrefix(line, "gitdir: ") {
 				gitDir := strings.TrimPrefix(line, "gitdir: ")
-				// Remove /worktrees/* part
-				if idx := strings.Index(gitDir, "/worktrees/"); idx > 0 {
+				// Remove /worktrees/* part - use LastIndex to handle user paths containing "worktrees"
+				// e.g., /Users/foo/worktrees/project/.bare/worktrees/main should strip at .bare/worktrees/
+				if idx := strings.LastIndex(gitDir, "/worktrees/"); idx > 0 {
 					gitDir = gitDir[:idx]
 				}
 				repoRoot = filepath.Dir(gitDir)