diff --git a/backend/internal/adapters/workspace/gitworktree/workspace.go b/backend/internal/adapters/workspace/gitworktree/workspace.go
index c1c7d8ed0..25c267dc1 100644
--- a/backend/internal/adapters/workspace/gitworktree/workspace.go
+++ b/backend/internal/adapters/workspace/gitworktree/workspace.go
@@ -611,6 +611,14 @@ func (w *Workspace) addWorktree(ctx context.Context, repo, path, branch, baseBra
 		return err
 	}
 	if _, err := w.run(ctx, w.binary, worktreeAddNewBranchArgs(repo, branch, path, baseRef)...); err != nil {
+		if isMissingRegisteredWorktreeError(err) {
+			if pruneErr := w.pruneWorktrees(ctx, repo); pruneErr != nil {
+				return fmt.Errorf("gitworktree: worktree add branch %q from %q: recover stale registration: %w", branch, baseRef, pruneErr)
+			}
+			if _, retryErr := w.run(ctx, w.binary, worktreeAddNewBranchArgs(repo, branch, path, baseRef)...); retryErr == nil {
+				return nil
+			}
+		}
 		return fmt.Errorf("gitworktree: worktree add branch %q from %q: %w", branch, baseRef, err)
 	}
 	return nil
@@ -681,6 +689,14 @@ func (w *Workspace) createWorkspaceProjectRepo(ctx context.Context, repo workspa
 		return "", err
 	}
 	if _, err := w.run(ctx, w.binary, worktreeAddNewBranchArgs(repo.repoPath, branch, repo.outputPath, baseRef)...); err != nil {
+		if isMissingRegisteredWorktreeError(err) {
+			if pruneErr := w.pruneWorktrees(ctx, repo.repoPath); pruneErr != nil {
+				return "", fmt.Errorf("gitworktree: workspace repo %q worktree add branch %q from %q: recover stale registration: %w", repo.name, branch, baseRef, pruneErr)
+			}
+			if _, retryErr := w.run(ctx, w.binary, worktreeAddNewBranchArgs(repo.repoPath, branch, repo.outputPath, baseRef)...); retryErr == nil {
+				return baseSHA, nil
+			}
+		}
 		return "", fmt.Errorf("gitworktree: workspace repo %q worktree add branch %q from %q: %w", repo.name, branch, baseRef, err)
 	}
 	return baseSHA, nil
@@ -688,8 +704,8 @@ func (w *Workspace) createWorkspaceProjectRepo(ctx context.Context, repo workspa
 
 func (w *Workspace) forceDestroyPath(ctx context.Context, repo, path string) error {
 	_, _ = w.run(ctx, w.binary, worktreeForceRemoveArgs(repo, path)...)
-	if _, err := w.run(ctx, w.binary, worktreePruneArgs(repo)...); err != nil {
-		return fmt.Errorf("gitworktree: worktree prune: %w", err)
+	if err := w.pruneWorktrees(ctx, repo); err != nil {
+		return err
 	}
 	if err := os.RemoveAll(path); err != nil {
 		return fmt.Errorf("gitworktree: force remove path %q: %w", path, err)
@@ -697,6 +713,17 @@ func (w *Workspace) forceDestroyPath(ctx context.Context, repo, path string) err
 	return nil
 }
 
+func (w *Workspace) pruneWorktrees(ctx context.Context, repo string) error {
+	if _, err := w.run(ctx, w.binary, worktreePruneArgs(repo)...); err != nil {
+		return fmt.Errorf("gitworktree: worktree prune: %w", err)
+	}
+	return nil
+}
+
+func isMissingRegisteredWorktreeError(err error) bool {
+	return strings.Contains(err.Error(), "is a missing but already registered worktree")
+}
+
 func (w *Workspace) revParse(ctx context.Context, repo, ref string) (string, error) {
 	out, err := w.run(ctx, w.binary, "-C", repo, "rev-parse", "--verify", ref)
 	if err != nil {
diff --git a/backend/internal/adapters/workspace/gitworktree/workspace_test.go b/backend/internal/adapters/workspace/gitworktree/workspace_test.go
index cf676ee11..3c557d2b8 100644
--- a/backend/internal/adapters/workspace/gitworktree/workspace_test.go
+++ b/backend/internal/adapters/workspace/gitworktree/workspace_test.go
@@ -211,6 +211,68 @@ func TestCreateReusesRegisteredWorktreeAtExpectedPath(t *testing.T) {
 	}
 }
 
+func TestCreateWorkspaceProjectRepoPrunesStaleRegisteredWorktree(t *testing.T) {
+	root := t.TempDir()
+	repo := t.TempDir()
+	output := filepath.Join(root, "proj", "orchestrator", "proj-orchestrator", "api")
+	ws, err := New(Options{ManagedRoot: root, RepoResolver: StaticRepoResolver{"proj": repo}})
+	if err != nil {
+		t.Fatalf("new: %v", err)
+	}
+	exitErr := exec.Command("sh", "-c", "exit 1").Run()
+	if exitErr == nil {
+		t.Fatal("expected exit error")
+	}
+	var calls []string
+	addAttempts := 0
+	ws.run = func(_ context.Context, binary string, args ...string) ([]byte, error) {
+		joined := strings.Join(args, " ")
+		calls = append(calls, joined)
+		switch {
+		case strings.Contains(joined, "rev-parse --verify --quiet origin/feature/test"):
+			return nil, commandError{args: append([]string{binary}, args...), err: exitErr}
+		case strings.Contains(joined, "rev-parse --verify --quiet origin/main"):
+			return nil, nil
+		case strings.Contains(joined, "rev-parse --verify origin/main"):
+			return []byte("abc123\n"), nil
+		case strings.Contains(joined, "worktree add -b feature/test "+output+" origin/main"):
+			addAttempts++
+			if addAttempts == 1 {
+				return nil, commandError{
+					args:   append([]string{binary}, args...),
+					output: "Preparing worktree (new branch 'feature/test')\nfatal: '" + output + "' is a missing but already registered worktree;\nuse 'add -f' to override, or 'prune' or 'remove' to clear",
+					err:    errors.New("exit status 128"),
+				}
+			}
+			return nil, nil
+		case strings.Contains(joined, "worktree prune"):
+			return nil, nil
+		default:
+			t.Fatalf("unexpected git invocation: %v", args)
+			return nil, nil
+		}
+	}
+
+	baseSHA, err := ws.createWorkspaceProjectRepo(context.Background(), workspaceProjectRepo{
+		name:       "api",
+		repoPath:   repo,
+		outputPath: output,
+	}, "feature/test")
+	if err != nil {
+		t.Fatalf("createWorkspaceProjectRepo: %v", err)
+	}
+	if baseSHA != "abc123" {
+		t.Fatalf("baseSHA = %q, want abc123", baseSHA)
+	}
+	if addAttempts != 2 {
+		t.Fatalf("add attempts = %d, want 2", addAttempts)
+	}
+	got := strings.Join(calls, "\n")
+	if !strings.Contains(got, "worktree prune") {
+		t.Fatalf("calls missing worktree prune:\n%s", got)
+	}
+}
+
 // TestValidateConfigRejectsPathEscapingIDs covers review item RB: filepath.Join
 // in managedPath cleans `..` segments before validateManagedPath sees them, so a
 // session id of "../other" would stay inside managedRoot while jumping projects.