diff --git a/README.md b/README.md
index cd90435..1ab3616 100644
--- a/README.md
+++ b/README.md
@@ -341,7 +341,9 @@ git may already have updated the checkout. It never deletes a lock itself.
 
 If the branch being deleted is the one you're on, sync switches you to its trunk first, and like
 `git switch` your uncommitted changes come along. It only keeps the branch when git says the
-switch would overwrite them, and then names the files.
+switch would overwrite them, and then names the files. A worktree whose directory you deleted
+by hand (rather than with `git worktree remove`) is forgotten at the start of the sync, so its
+branches can be cleaned up like any other; a locked one is left alone with a notice.
 
 Flags:
 - `-d` / `--delete-all` delete merged or closed branches without asking
diff --git a/docs/architecture.md b/docs/architecture.md
index c18fe53..e6e9293 100644
--- a/docs/architecture.md
+++ b/docs/architecture.md
@@ -272,7 +272,11 @@ dropped then, so it heals over two syncs. A candidate checked out in the current
 trunk is checked out in another worktree leaves HEAD detached at the trunk tip rather than
 failing. Moving the current checkout off a branch being deleted is a plain `git switch`, so
 uncommitted changes git can carry come along; only git's "would be overwritten" refusal keeps
-the branch (as `dirty`, files named); any other failure stops the sync as before. Consent for deletion is `stack.sync.prune` (`always` by default), `-d`, or `-f`;
+the branch (as `dirty`, files named); any other failure stops the sync as before. Before any of
+this, sync runs `git worktree prune` when `git worktree list` marks an entry prunable (its
+directory was deleted by hand): otherwise git still counts its branch as checked out there and
+the branch could never be deleted. Locked worktrees are never pruned, matching git; one whose
+directory is gone gets a notice to unlock it. Consent for deletion is `stack.sync.prune` (`always` by default), `-d`, or `-f`;
 with no terminal and `ask`, branches are kept with a notice. Nothing is pushed; `submit`
 does that.
 
diff --git a/pkg/app/sync.go b/pkg/app/sync.go
index 044216a..e7432d7 100644
--- a/pkg/app/sync.go
+++ b/pkg/app/sync.go
@@ -193,6 +193,9 @@ func (a *App) Sync(ctx context.Context, repo git.Repo, o SyncOptions) (SyncResul
 		return res, err
 	}
 	res.Remote = st.remote
+	if err := a.syncPruneWorktrees(ctx, st, &res); err != nil {
+		return res, err
+	}
 
 	// Listing pull requests is a forge round trip that can take longer than
 	// the fetch itself on a busy repository, so it runs alongside the fetch
@@ -290,7 +293,7 @@ func (a *App) gatherSync(ctx context.Context, repo git.Repo) (*syncState, error)
 	if err != nil {
 		return nil, err
 	}
-	st := &syncState{repo: repo, graph: graph, dirty: newDirtyCache(), local: map[string]git.Branch{}}
+	st := &syncState{repo: repo, graph: graph, dirty: newDirtyCache()}
 	st.trunks = graph.Trunks
 	if len(st.trunks) == 0 {
 		def, ok, err := a.d.Git.DefaultBranch(ctx, repo)
@@ -304,17 +307,25 @@ func (a *App) gatherSync(ctx context.Context, repo git.Repo) (*syncState, error)
 		st.trunks = []string{def}
 	}
 	st.remote = a.d.Git.RemoteFor(ctx, repo, st.trunks[0])
-	branches, err := a.d.Git.Branches(ctx, repo)
-	if err != nil {
+	if err := a.loadCheckouts(ctx, st); err != nil {
 		return nil, err
 	}
+	return st, nil
+}
+
+// loadCheckouts reads every local branch, with its tip and where it is
+// checked out, and the worktrees.
+func (a *App) loadCheckouts(ctx context.Context, st *syncState) error {
+	branches, err := a.d.Git.Branches(ctx, st.repo)
+	if err != nil {
+		return err
+	}
+	st.local = make(map[string]git.Branch, len(branches))
 	for _, b := range branches {
 		st.local[b.Name] = b
 	}
-	if st.worktrees, err = a.d.Git.Worktrees(ctx, repo); err != nil {
-		return nil, err
-	}
-	return st, nil
+	st.worktrees, err = a.d.Git.Worktrees(ctx, st.repo)
+	return err
 }
 
 // moveBranch moves a local branch from one tip to another. A branch nobody
diff --git a/pkg/app/sync_cleanup_test.go b/pkg/app/sync_cleanup_test.go
index 33c44f7..1ad7d7e 100644
--- a/pkg/app/sync_cleanup_test.go
+++ b/pkg/app/sync_cleanup_test.go
@@ -2,6 +2,7 @@ package app_test
 
 import (
 	"context"
+	"os"
 	"path/filepath"
 	"slices"
 	"strings"
@@ -416,6 +417,52 @@ func TestSyncKeepsDeletedBranchWhenSwitchWouldOverwriteChanges(t *testing.T) {
 	}
 }
 
+func TestSyncPrunesWorktreeWhoseDirectoryIsGone(t *testing.T) {
+	f := newSyncFixture(t)
+	gittest.Run(t, f.dir, "switch", "-q", "main")
+	wt := filepath.Join(t.TempDir(), "wt")
+	gittest.Run(t, f.dir, "worktree", "add", "-q", wt, "a")
+	if err := os.RemoveAll(wt); err != nil {
+		t.Fatal(err)
+	}
+	f.mergeOnRemote(t, "a", 0)
+	res, err := f.sync(t, app.SyncOptions{NoRestack: true})
+	if err != nil {
+		t.Fatal(err)
+	}
+	if _, ok := deleted(res, "a"); !ok || branchExists(t, f.dir, "a") {
+		t.Errorf("a should be deleted once its dead worktree is pruned: deleted = %+v kept = %+v", res.Deleted, res.Kept)
+	}
+	if n := len(strings.Split(gittest.Run(t, f.dir, "worktree", "list"), "\n")); n != 1 {
+		t.Errorf("%d worktrees left, want just the main one", n)
+	}
+	if !strings.Contains(strings.Join(res.Notices, "\n"), "its directory is gone") {
+		t.Errorf("notices = %v", res.Notices)
+	}
+}
+
+func TestSyncLeavesLockedWorktreeWhoseDirectoryIsGone(t *testing.T) {
+	f := newSyncFixture(t)
+	gittest.Run(t, f.dir, "switch", "-q", "main")
+	wt := filepath.Join(t.TempDir(), "wt")
+	gittest.Run(t, f.dir, "worktree", "add", "-q", wt, "a")
+	gittest.Run(t, f.dir, "worktree", "lock", wt)
+	if err := os.RemoveAll(wt); err != nil {
+		t.Fatal(err)
+	}
+	f.mergeOnRemote(t, "a", 0)
+	res, err := f.sync(t, app.SyncOptions{NoRestack: true})
+	if err != nil {
+		t.Fatal(err)
+	}
+	if k, ok := kept(res, "a"); !ok || k.Reason != app.KeptOtherWorktree || !branchExists(t, f.dir, "a") {
+		t.Errorf("kept = %+v", res.Kept)
+	}
+	if !strings.Contains(strings.Join(res.Notices, "\n"), "git worktree unlock") {
+		t.Errorf("notices = %v", res.Notices)
+	}
+}
+
 func TestSyncDropsGoneBranchesFromMetadata(t *testing.T) {
 	f := newSyncFixture(t)
 	f.deps.Config.SyncPrune = config.SyncPruneNever
diff --git a/pkg/app/sync_worktrees.go b/pkg/app/sync_worktrees.go
new file mode 100644
index 0000000..b4f6dcb
--- /dev/null
+++ b/pkg/app/sync_worktrees.go
@@ -0,0 +1,43 @@
+package app
+
+import (
+	"context"
+	"errors"
+	"io/fs"
+	"os"
+)
+
+// syncPruneWorktrees forgets worktrees whose directory was deleted without
+// git worktree remove. git still counts their branches as checked out
+// there, so until they are pruned sync would keep those branches and say to
+// sync from a directory that no longer exists. A locked worktree is never
+// pruned (that's what the lock is for, e.g. a checkout on a drive that isn't
+// mounted), so it only gets a notice.
+func (a *App) syncPruneWorktrees(ctx context.Context, st *syncState, res *SyncResult) error {
+	var gone []string
+	for _, wt := range st.worktrees {
+		switch {
+		case wt.Prunable && !wt.Locked:
+			gone = append(gone, wt.Path)
+		case wt.Locked && missing(wt.Path):
+			res.notice("the worktree at %s is locked, so git keeps it although its directory is gone; run git worktree unlock %s and sync again to clean it up",
+				shortPath(wt.Path), wt.Path)
+		}
+	}
+	if len(gone) == 0 {
+		return nil
+	}
+	if err := a.d.Git.PruneWorktrees(ctx, st.repo); err != nil {
+		return err
+	}
+	for _, p := range gone {
+		res.notice("forgot the worktree at %s because its directory is gone", shortPath(p))
+	}
+	return a.loadCheckouts(ctx, st)
+}
+
+// missing reports whether nothing exists at path.
+func missing(path string) bool {
+	_, err := os.Stat(path)
+	return errors.Is(err, fs.ErrNotExist)
+}
diff --git a/pkg/git/branch.go b/pkg/git/branch.go
index 60ed213..3640c1c 100644
--- a/pkg/git/branch.go
+++ b/pkg/git/branch.go
@@ -137,6 +137,19 @@ func (c *Client) SwitchDetached(ctx context.Context, repo Repo, rev string) erro
 	return nil
 }
 
+// PruneWorktrees forgets every worktree whose directory is gone, the way
+// git worktree prune does. Locked ones are left alone.
+func (c *Client) PruneWorktrees(ctx context.Context, repo Repo) error {
+	_, err := c.gitIn(ctx, repo, "worktree", "prune")
+	if err != nil {
+		if ee, ok := errors.AsType[*exec.ExitError](err); ok {
+			return fmt.Errorf("worktree prune: %s", ee.Result.Err())
+		}
+		return err
+	}
+	return nil
+}
+
 // Worktree is one entry of `git worktree list`.
 type Worktree struct {
 	// Path is the working tree root.
@@ -146,6 +159,11 @@ type Worktree struct {
 	Branch   string
 	Detached bool
 	Bare     bool
+	// Prunable is set when git would prune the entry, usually because its
+	// directory has been deleted.
+	Prunable bool
+	// Locked is set when the entry is locked against pruning.
+	Locked bool
 }
 
 // Worktrees lists the main checkout and every linked worktree.
@@ -180,6 +198,10 @@ func (c *Client) Worktrees(ctx context.Context, repo Repo) ([]Worktree, error) {
 			cur.Detached = true
 		case line == "bare":
 			cur.Bare = true
+		case line == "prunable" || strings.HasPrefix(line, "prunable "):
+			cur.Prunable = true
+		case line == "locked" || strings.HasPrefix(line, "locked "):
+			cur.Locked = true
 		}
 	}
 	flush()
diff --git a/pkg/git/worktree_test.go b/pkg/git/worktree_test.go
index d5fbbc4..1cd443d 100644
--- a/pkg/git/worktree_test.go
+++ b/pkg/git/worktree_test.go
@@ -3,6 +3,7 @@ package git_test
 import (
 	"context"
 	"errors"
+	"os"
 	"path/filepath"
 	"testing"
 
@@ -42,6 +43,47 @@ func TestWorktrees(t *testing.T) {
 	}
 }
 
+func TestWorktreesMarksMissingDirectoriesPrunable(t *testing.T) {
+	gittest.Isolate(t)
+	dir := gittest.InitRepo(t)
+	c := newClient()
+	ctx := context.Background()
+	repo, err := c.Discover(ctx, dir)
+	if err != nil {
+		t.Fatal(err)
+	}
+	gone := filepath.Join(t.TempDir(), "gone")
+	gittest.Run(t, dir, "worktree", "add", "-q", "-b", "gone", gone)
+	locked := filepath.Join(t.TempDir(), "locked")
+	gittest.Run(t, dir, "worktree", "add", "-q", "-b", "locked", locked)
+	gittest.Run(t, dir, "worktree", "lock", "--reason", "on a usb stick", locked)
+	for _, p := range []string{gone, locked} {
+		if err := os.RemoveAll(p); err != nil {
+			t.Fatal(err)
+		}
+	}
+
+	wts, err := c.Worktrees(ctx, repo)
+	if err != nil {
+		t.Fatal(err)
+	}
+	// git never offers a locked worktree for pruning, gone or not.
+	if len(wts) != 3 || wts[0].Prunable || !wts[1].Prunable || wts[1].Locked || wts[2].Prunable || !wts[2].Locked {
+		t.Fatalf("worktrees = %+v", wts)
+	}
+
+	if err := c.PruneWorktrees(ctx, repo); err != nil {
+		t.Fatal(err)
+	}
+	wts, err = c.Worktrees(ctx, repo)
+	if err != nil {
+		t.Fatal(err)
+	}
+	if len(wts) != 2 || wts[1].Branch != "locked" {
+		t.Errorf("after prune = %+v; want the locked one kept", wts)
+	}
+}
+
 func TestSwitchReportsFilesInTheWay(t *testing.T) {
 	gittest.Isolate(t)
 	dir := gittest.InitRepo(t)