diff --git a/internal/syncbranch/worktree.go b/internal/syncbranch/worktree.go
index 372d0d50..bb76ebd7 100644
--- a/internal/syncbranch/worktree.go
+++ b/internal/syncbranch/worktree.go
@@ -77,8 +77,8 @@ func CommitToSyncBranch(ctx context.Context, repoRoot, syncBranch, jsonlPath str
 		Branch: syncBranch,
 	}
 
-	// Worktree path is under .git/beads-worktrees/<branch>
-	worktreePath := filepath.Join(repoRoot, ".git", "beads-worktrees", syncBranch)
+	// GH#639: Use git-common-dir for worktree path to support bare repos
+	worktreePath := getBeadsWorktreePath(ctx, repoRoot, syncBranch)
 
 	// Initialize worktree manager
 	wtMgr := git.NewWorktreeManager(repoRoot)
@@ -240,8 +240,8 @@ func PullFromSyncBranch(ctx context.Context, repoRoot, syncBranch, jsonlPath str
 		JSONLPath: jsonlPath,
 	}
 
-	// Worktree path is under .git/beads-worktrees/<branch>
-	worktreePath := filepath.Join(repoRoot, ".git", "beads-worktrees", syncBranch)
+	// GH#639: Use git-common-dir for worktree path to support bare repos
+	worktreePath := getBeadsWorktreePath(ctx, repoRoot, syncBranch)
 
 	// Initialize worktree manager
 	wtMgr := git.NewWorktreeManager(repoRoot)
@@ -469,8 +469,8 @@ func CheckDivergence(ctx context.Context, repoRoot, syncBranch string) (*Diverge
 		Branch: syncBranch,
 	}
 
-	// Worktree path is under .git/beads-worktrees/<branch>
-	worktreePath := filepath.Join(repoRoot, ".git", "beads-worktrees", syncBranch)
+	// GH#639: Use git-common-dir for worktree path to support bare repos
+	worktreePath := getBeadsWorktreePath(ctx, repoRoot, syncBranch)
 
 	// Initialize worktree manager
 	wtMgr := git.NewWorktreeManager(repoRoot)
@@ -526,8 +526,8 @@ func CheckDivergence(ctx context.Context, repoRoot, syncBranch string) (*Diverge
 //
 // Returns error if reset fails.
 func ResetToRemote(ctx context.Context, repoRoot, syncBranch, jsonlPath string) error {
-	// Worktree path is under .git/beads-worktrees/<branch>
-	worktreePath := filepath.Join(repoRoot, ".git", "beads-worktrees", syncBranch)
+	// GH#639: Use git-common-dir for worktree path to support bare repos
+	worktreePath := getBeadsWorktreePath(ctx, repoRoot, syncBranch)
 
 	// Initialize worktree manager
 	wtMgr := git.NewWorktreeManager(repoRoot)
@@ -858,6 +858,28 @@ func PushSyncBranch(ctx context.Context, repoRoot, syncBranch string) error {
 	return pushFromWorktree(ctx, worktreePath, syncBranch)
 }
 
+// getBeadsWorktreePath returns the path where beads worktrees should be stored.
+// GH#639: Uses git rev-parse --git-common-dir to correctly handle bare repos and worktrees.
+// For regular repos, this is typically .git/beads-worktrees/<branch>.
+// For bare repos or worktrees of bare repos, this uses the common git directory.
+func getBeadsWorktreePath(ctx context.Context, repoRoot, syncBranch string) string {
+	// Try to get the git common directory using git's native API
+	// This handles all cases: regular repos, worktrees, bare repos
+	cmd := exec.CommandContext(ctx, "git", "-C", repoRoot, "rev-parse", "--git-common-dir")
+	output, err := cmd.Output()
+	if err == nil {
+		gitCommonDir := strings.TrimSpace(string(output))
+		// Make path absolute if it's relative
+		if !filepath.IsAbs(gitCommonDir) {
+			gitCommonDir = filepath.Join(repoRoot, gitCommonDir)
+		}
+		return filepath.Join(gitCommonDir, "beads-worktrees", syncBranch)
+	}
+
+	// Fallback to legacy behavior for compatibility
+	return filepath.Join(repoRoot, ".git", "beads-worktrees", syncBranch)
+}
+
 // getRemoteForBranch gets the remote name for a branch, defaulting to "origin"
 func getRemoteForBranch(ctx context.Context, worktreePath, branch string) string {
 	remoteCmd := exec.CommandContext(ctx, "git", "-C", worktreePath, "config", "--get", fmt.Sprintf("branch.%s.remote", branch))
diff --git a/internal/syncbranch/worktree_path_test.go b/internal/syncbranch/worktree_path_test.go
new file mode 100644
index 00000000..edc824c3
--- /dev/null
+++ b/internal/syncbranch/worktree_path_test.go
@@ -0,0 +1,174 @@
+package syncbranch
+
+import (
+	"context"
+	"os"
+	"os/exec"
+	"path/filepath"
+	"strings"
+	"testing"
+)
+
+// TestGetBeadsWorktreePath tests the worktree path calculation for various repo structures.
+// This is the regression test for GH#639.
+func TestGetBeadsWorktreePath(t *testing.T) {
+	if testing.Short() {
+		t.Skip("Skipping integration test in short mode")
+	}
+
+	ctx := context.Background()
+
+	t.Run("regular repo returns .git/beads-worktrees path", func(t *testing.T) {
+		// Create a regular git repository
+		tmpDir := t.TempDir()
+		runGitCmd(t, tmpDir, "init")
+		runGitCmd(t, tmpDir, "config", "user.email", "test@test.com")
+		runGitCmd(t, tmpDir, "config", "user.name", "Test User")
+
+		// Create initial commit
+		testFile := filepath.Join(tmpDir, "test.txt")
+		if err := os.WriteFile(testFile, []byte("test"), 0644); err != nil {
+			t.Fatalf("Failed to write test file: %v", err)
+		}
+		runGitCmd(t, tmpDir, "add", ".")
+		runGitCmd(t, tmpDir, "commit", "-m", "initial")
+
+		// Test getBeadsWorktreePath
+		path := getBeadsWorktreePath(ctx, tmpDir, "beads-sync")
+
+		// Should be under .git/beads-worktrees
+		expectedSuffix := filepath.Join(".git", "beads-worktrees", "beads-sync")
+		if !strings.HasSuffix(path, expectedSuffix) {
+			t.Errorf("Expected path to end with %q, got %q", expectedSuffix, path)
+		}
+
+		// Path should be absolute
+		if !filepath.IsAbs(path) {
+			t.Errorf("Expected absolute path, got %q", path)
+		}
+	})
+
+	t.Run("bare repo returns correct worktree path", func(t *testing.T) {
+		// Create a bare repository
+		tmpDir := t.TempDir()
+		bareRepoPath := filepath.Join(tmpDir, "bare.git")
+		runGitCmd(t, tmpDir, "init", "--bare", bareRepoPath)
+
+		// Test getBeadsWorktreePath from bare repo
+		path := getBeadsWorktreePath(ctx, bareRepoPath, "beads-sync")
+
+		// For bare repos, git-common-dir returns the bare repo itself
+		// So the path should be <bare-repo>/beads-worktrees/beads-sync
+		expectedPath := filepath.Join(bareRepoPath, "beads-worktrees", "beads-sync")
+		if path != expectedPath {
+			t.Errorf("Expected path %q, got %q", expectedPath, path)
+		}
+
+		// Path should be absolute
+		if !filepath.IsAbs(path) {
+			t.Errorf("Expected absolute path, got %q", path)
+		}
+
+		// Verify it's NOT trying to create .git/beads-worktrees inside the bare repo
+		// (which would fail since bare repos don't have a .git subdirectory)
+		badPath := filepath.Join(bareRepoPath, ".git", "beads-worktrees", "beads-sync")
+		if path == badPath {
+			t.Errorf("Bare repo should not use .git subdirectory path: %q", path)
+		}
+	})
+
+	t.Run("worktree of regular repo uses common git dir", func(t *testing.T) {
+		// Create a regular repository
+		tmpDir := t.TempDir()
+		mainRepoPath := filepath.Join(tmpDir, "main-repo")
+		if err := os.MkdirAll(mainRepoPath, 0750); err != nil {
+			t.Fatalf("Failed to create main repo dir: %v", err)
+		}
+
+		runGitCmd(t, mainRepoPath, "init")
+		runGitCmd(t, mainRepoPath, "config", "user.email", "test@test.com")
+		runGitCmd(t, mainRepoPath, "config", "user.name", "Test User")
+
+		// Create initial commit
+		testFile := filepath.Join(mainRepoPath, "test.txt")
+		if err := os.WriteFile(testFile, []byte("test"), 0644); err != nil {
+			t.Fatalf("Failed to write test file: %v", err)
+		}
+		runGitCmd(t, mainRepoPath, "add", ".")
+		runGitCmd(t, mainRepoPath, "commit", "-m", "initial")
+
+		// Create a worktree
+		worktreePath := filepath.Join(tmpDir, "feature-worktree")
+		runGitCmd(t, mainRepoPath, "worktree", "add", worktreePath, "-b", "feature")
+
+		// Test getBeadsWorktreePath from the worktree
+		path := getBeadsWorktreePath(ctx, worktreePath, "beads-sync")
+
+		// Should point to the main repo's .git/beads-worktrees, not the worktree's
+		mainGitDir := filepath.Join(mainRepoPath, ".git")
+		expectedPath := filepath.Join(mainGitDir, "beads-worktrees", "beads-sync")
+		if path != expectedPath {
+			t.Errorf("Expected path %q, got %q", expectedPath, path)
+		}
+	})
+
+	t.Run("fallback works when git command fails", func(t *testing.T) {
+		// Test with a non-git directory (should fallback to legacy behavior)
+		tmpDir := t.TempDir()
+
+		path := getBeadsWorktreePath(ctx, tmpDir, "beads-sync")
+
+		// Should fallback to legacy .git/beads-worktrees path
+		expectedPath := filepath.Join(tmpDir, ".git", "beads-worktrees", "beads-sync")
+		if path != expectedPath {
+			t.Errorf("Expected fallback path %q, got %q", expectedPath, path)
+		}
+	})
+}
+
+// TestGetBeadsWorktreePathRelativePath tests that relative paths from git are handled correctly
+func TestGetBeadsWorktreePathRelativePath(t *testing.T) {
+	if testing.Short() {
+		t.Skip("Skipping integration test in short mode")
+	}
+
+	ctx := context.Background()
+
+	// Create a regular git repository
+	tmpDir := t.TempDir()
+	runGitCmd(t, tmpDir, "init")
+	runGitCmd(t, tmpDir, "config", "user.email", "test@test.com")
+	runGitCmd(t, tmpDir, "config", "user.name", "Test User")
+
+	// Create initial commit
+	testFile := filepath.Join(tmpDir, "test.txt")
+	if err := os.WriteFile(testFile, []byte("test"), 0644); err != nil {
+		t.Fatalf("Failed to write test file: %v", err)
+	}
+	runGitCmd(t, tmpDir, "add", ".")
+	runGitCmd(t, tmpDir, "commit", "-m", "initial")
+
+	// Test from a subdirectory
+	subDir := filepath.Join(tmpDir, "subdir")
+	if err := os.MkdirAll(subDir, 0750); err != nil {
+		t.Fatalf("Failed to create subdir: %v", err)
+	}
+
+	// getBeadsWorktreePath should still return an absolute path
+	path := getBeadsWorktreePath(ctx, subDir, "beads-sync")
+
+	if !filepath.IsAbs(path) {
+		t.Errorf("Expected absolute path, got %q", path)
+	}
+}
+
+// runGitCmd is a helper to run git commands
+func runGitCmd(t *testing.T, dir string, args ...string) {
+	t.Helper()
+	cmd := exec.Command("git", args...)
+	cmd.Dir = dir
+	output, err := cmd.CombinedOutput()
+	if err != nil {
+		t.Fatalf("git %v failed: %v\n%s", args, err, output)
+	}
+}