diff --git a/internal/git/worktree.go b/internal/git/worktree.go
index 9d432003..754ec92d 100644
--- a/internal/git/worktree.go
+++ b/internal/git/worktree.go
@@ -181,11 +181,15 @@ func (wm *WorktreeManager) SyncJSONLToWorktree(worktreePath, jsonlRelPath string
 // If ForceOverwrite is false (default), the function uses merge logic to prevent
 // data loss when a fresh clone syncs with fewer issues than the remote.
 func (wm *WorktreeManager) SyncJSONLToWorktreeWithOptions(worktreePath, jsonlRelPath string, opts SyncOptions) error {
-	// Source: main repo JSONL
+	// Source: main repo JSONL (use the full path as provided)
 	srcPath := filepath.Join(wm.repoPath, jsonlRelPath)
 
 	// Destination: worktree JSONL
-	dstPath := filepath.Join(worktreePath, jsonlRelPath)
+	// GH#785: Handle bare repo worktrees where jsonlRelPath might include the
+	// worktree name (e.g., "main/.beads/issues.jsonl"). The sync branch uses
+	// sparse checkout for .beads/* so we normalize to strip leading components.
+	normalizedRelPath := normalizeBeadsRelPath(jsonlRelPath)
+	dstPath := filepath.Join(worktreePath, normalizedRelPath)
 
 	// Ensure destination directory exists
 	dstDir := filepath.Dir(dstPath)
@@ -317,6 +321,20 @@ func (wm *WorktreeManager) mergeJSONLFiles(srcData, dstData []byte) ([]byte, err
 }
 
 
+// normalizeBeadsRelPath strips any leading path components before .beads.
+// This handles bare repo worktrees where the relative path includes the worktree
+// name (e.g., "main/.beads/issues.jsonl" -> ".beads/issues.jsonl").
+// GH#785: Fix for sync failing across worktrees in bare repo setup.
+func normalizeBeadsRelPath(relPath string) string {
+	// Use filepath.ToSlash for consistent handling across platforms
+	normalized := filepath.ToSlash(relPath)
+	if idx := strings.Index(normalized, ".beads"); idx > 0 {
+		// Strip leading path components before .beads
+		return filepath.FromSlash(normalized[idx:])
+	}
+	return relPath
+}
+
 // isValidWorktree checks if the path is a valid git worktree
 func (wm *WorktreeManager) isValidWorktree(worktreePath string) (bool, error) {
 	cmd := exec.Command("git", "worktree", "list", "--porcelain")
diff --git a/internal/syncbranch/worktree.go b/internal/syncbranch/worktree.go
index 918d3a1d..7ab233fe 100644
--- a/internal/syncbranch/worktree.go
+++ b/internal/syncbranch/worktree.go
@@ -656,7 +656,12 @@ func extractJSONLFromCommit(ctx context.Context, worktreePath, commit, filePath
 
 // copyJSONLToMainRepo copies JSONL and related files from worktree to main repo.
 func copyJSONLToMainRepo(worktreePath, jsonlRelPath, jsonlPath string) error {
-	worktreeJSONLPath := filepath.Join(worktreePath, jsonlRelPath)
+	// GH#785: Handle bare repo worktrees where jsonlRelPath might include the
+	// worktree name (e.g., "main/.beads/issues.jsonl" instead of ".beads/issues.jsonl").
+	// The sync branch uses sparse checkout for .beads/* so we normalize the path
+	// to strip any leading components before .beads.
+	normalizedRelPath := normalizeBeadsRelPath(jsonlRelPath)
+	worktreeJSONLPath := filepath.Join(worktreePath, normalizedRelPath)
 
 	// Check if worktree JSONL exists
 	if _, err := os.Stat(worktreeJSONLPath); os.IsNotExist(err) {
@@ -1077,6 +1082,20 @@ func formatVanishedIssues(localIssues, mergedIssues map[string]issueSummary, loc
 	return lines
 }
 
+// normalizeBeadsRelPath strips any leading path components before .beads.
+// This handles bare repo worktrees where the relative path includes the worktree
+// name (e.g., "main/.beads/issues.jsonl" -> ".beads/issues.jsonl").
+// GH#785: Fix for sync failing across worktrees in bare repo setup.
+func normalizeBeadsRelPath(relPath string) string {
+	// Use filepath.ToSlash for consistent handling across platforms
+	normalized := filepath.ToSlash(relPath)
+	if idx := strings.Index(normalized, ".beads"); idx > 0 {
+		// Strip leading path components before .beads
+		return filepath.FromSlash(normalized[idx:])
+	}
+	return relPath
+}
+
 // HasGitRemote checks if any git remote exists
 func HasGitRemote(ctx context.Context) bool {
 	cmd := exec.CommandContext(ctx, "git", "remote")
diff --git a/internal/syncbranch/worktree_path_test.go b/internal/syncbranch/worktree_path_test.go
index 5938b891..77d973de 100644
--- a/internal/syncbranch/worktree_path_test.go
+++ b/internal/syncbranch/worktree_path_test.go
@@ -179,3 +179,56 @@ func runGitCmd(t *testing.T, dir string, args ...string) {
 		t.Fatalf("git %v failed: %v\n%s", args, err, output)
 	}
 }
+
+// TestNormalizeBeadsRelPath tests path normalization for bare repo worktrees.
+// This is the regression test for GH#785.
+func TestNormalizeBeadsRelPath(t *testing.T) {
+	tests := []struct {
+		name     string
+		input    string
+		expected string
+	}{
+		{
+			name:     "normal repo path unchanged",
+			input:    ".beads/issues.jsonl",
+			expected: ".beads/issues.jsonl",
+		},
+		{
+			name:     "bare repo worktree strips leading component",
+			input:    "main/.beads/issues.jsonl",
+			expected: ".beads/issues.jsonl",
+		},
+		{
+			name:     "bare repo worktree with deeper path",
+			input:    "worktrees/feature-branch/.beads/issues.jsonl",
+			expected: ".beads/issues.jsonl",
+		},
+		{
+			name:     "metadata file also works",
+			input:    "main/.beads/metadata.json",
+			expected: ".beads/metadata.json",
+		},
+		{
+			name:     "path with no .beads unchanged",
+			input:    "some/other/path.txt",
+			expected: "some/other/path.txt",
+		},
+		{
+			name:     ".beads at start unchanged",
+			input:    ".beads/subdir/file.jsonl",
+			expected: ".beads/subdir/file.jsonl",
+		},
+	}
+
+	for _, tt := range tests {
+		t.Run(tt.name, func(t *testing.T) {
+			// Normalize to forward slashes for comparison
+			result := normalizeBeadsRelPath(tt.input)
+			// Convert expected to platform path for comparison
+			expectedPlatform := filepath.FromSlash(tt.expected)
+			if result != expectedPlatform {
+				t.Errorf("normalizeBeadsRelPath(%q) = %q, want %q", tt.input, result, expectedPlatform)
+			}
+		})
+	}
+}