diff --git a/cmd/bd/daemon_sync_branch.go b/cmd/bd/daemon_sync_branch.go
index ac002689..f50b5873 100644
--- a/cmd/bd/daemon_sync_branch.go
+++ b/cmd/bd/daemon_sync_branch.go
@@ -161,7 +161,8 @@ func gitCommitInWorktree(ctx context.Context, worktreePath, filePath, message st
 	}
 
 	// Stage the file
-	addCmd := exec.CommandContext(ctx, "git", "-C", worktreePath, "add", relPath) // #nosec G204 - worktreePath and relPath are derived from trusted git operations
+	// Use --sparse to work correctly with sparse-checkout enabled worktrees (fixes #1076)
+	addCmd := exec.CommandContext(ctx, "git", "-C", worktreePath, "add", "--sparse", relPath) // #nosec G204 - worktreePath and relPath are derived from trusted git operations
 	if err := addCmd.Run(); err != nil {
 		return fmt.Errorf("git add failed in worktree: %w", err)
 	}
diff --git a/cmd/bd/migrate_sync.go b/cmd/bd/migrate_sync.go
index 5b95f1a8..1546fc03 100644
--- a/cmd/bd/migrate_sync.go
+++ b/cmd/bd/migrate_sync.go
@@ -339,7 +339,8 @@ func commitInitialSyncState(ctx context.Context, worktreePath, jsonlRelPath stri
 	beadsRelDir := filepath.Dir(jsonlRelPath)
 
 	// Stage all beads files
-	addCmd := exec.CommandContext(ctx, "git", "-C", worktreePath, "add", beadsRelDir)
+	// Use --sparse to work correctly with sparse-checkout enabled worktrees (fixes #1076)
+	addCmd := exec.CommandContext(ctx, "git", "-C", worktreePath, "add", "--sparse", beadsRelDir)
 	if err := addCmd.Run(); err != nil {
 		return fmt.Errorf("git add failed: %w", err)
 	}
diff --git a/cmd/bd/sync_branch.go b/cmd/bd/sync_branch.go
index c109c5aa..a7f2a9ab 100644
--- a/cmd/bd/sync_branch.go
+++ b/cmd/bd/sync_branch.go
@@ -304,7 +304,8 @@ func commitToExternalBeadsRepo(ctx context.Context, beadsDir, message string, pu
 		relBeadsDir = beadsDir // Fallback to absolute path
 	}
 
-	addCmd := exec.CommandContext(ctx, "git", "-C", repoRoot, "add", relBeadsDir) //nolint:gosec // paths from trusted sources
+	// Use --sparse to work correctly with sparse-checkout enabled worktrees (fixes #1076)
+	addCmd := exec.CommandContext(ctx, "git", "-C", repoRoot, "add", "--sparse", relBeadsDir) //nolint:gosec // paths from trusted sources
 	if output, err := addCmd.CombinedOutput(); err != nil {
 		return false, fmt.Errorf("git add failed: %w\n%s", err, output)
 	}
diff --git a/internal/syncbranch/worktree.go b/internal/syncbranch/worktree.go
index 485a486a..664d0a3f 100644
--- a/internal/syncbranch/worktree.go
+++ b/internal/syncbranch/worktree.go
@@ -728,7 +728,8 @@ func commitInWorktree(ctx context.Context, worktreePath, jsonlRelPath, message s
 
 	// Use -f (force) to add files even if they're gitignored
 	// In contributor mode, .beads/ is excluded in .git/info/exclude but needs to be tracked in sync branch
-	addCmd := exec.CommandContext(ctx, "git", "-C", worktreePath, "add", "-f", beadsRelDir)
+	// Use --sparse to work correctly with sparse-checkout enabled worktrees (fixes #1076)
+	addCmd := exec.CommandContext(ctx, "git", "-C", worktreePath, "add", "-f", "--sparse", beadsRelDir)
 	if err := addCmd.Run(); err != nil {
 		return fmt.Errorf("git add failed in worktree: %w", err)
 	}