diff --git a/internal/git/worktree.go b/internal/git/worktree.go
index 754ec92d..bd0e011f 100644
--- a/internal/git/worktree.go
+++ b/internal/git/worktree.go
@@ -321,14 +321,15 @@ func (wm *WorktreeManager) mergeJSONLFiles(srcData, dstData []byte) ([]byte, err
 }
 
 
-// normalizeBeadsRelPath strips any leading path components before .beads.
+// 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 {
+	// Look for ".beads/" to ensure we match the directory, not a prefix like ".beads-backup"
+	if idx := strings.Index(normalized, ".beads/"); idx > 0 {
 		// Strip leading path components before .beads
 		return filepath.FromSlash(normalized[idx:])
 	}
diff --git a/internal/syncbranch/worktree.go b/internal/syncbranch/worktree.go
index 7ab233fe..d5956b99 100644
--- a/internal/syncbranch/worktree.go
+++ b/internal/syncbranch/worktree.go
@@ -1082,14 +1082,15 @@ func formatVanishedIssues(localIssues, mergedIssues map[string]issueSummary, loc
 	return lines
 }
 
-// normalizeBeadsRelPath strips any leading path components before .beads.
+// 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 {
+	// Look for ".beads/" to ensure we match the directory, not a prefix like ".beads-backup"
+	if idx := strings.Index(normalized, ".beads/"); idx > 0 {
 		// Strip leading path components before .beads
 		return filepath.FromSlash(normalized[idx:])
 	}
diff --git a/internal/syncbranch/worktree_path_test.go b/internal/syncbranch/worktree_path_test.go
index 77d973de..6904d45b 100644
--- a/internal/syncbranch/worktree_path_test.go
+++ b/internal/syncbranch/worktree_path_test.go
@@ -218,6 +218,16 @@ func TestNormalizeBeadsRelPath(t *testing.T) {
 			input:    ".beads/subdir/file.jsonl",
 			expected: ".beads/subdir/file.jsonl",
 		},
+		{
+			name:     "similar prefix like .beads-backup not matched",
+			input:    "foo/.beads-backup/.beads/issues.jsonl",
+			expected: ".beads/issues.jsonl",
+		},
+		{
+			name:     "only .beads-backup no real .beads unchanged",
+			input:    "foo/.beads-backup/file.txt",
+			expected: "foo/.beads-backup/file.txt",
+		},
 	}
 
 	for _, tt := range tests {