diff --git a/internal/sites/sites.go b/internal/sites/sites.go
index a6d98db..7d274eb 100644
--- a/internal/sites/sites.go
+++ b/internal/sites/sites.go
@@ -100,6 +100,22 @@ func (m *Manager) Sync() error {
 	if err != nil {
 		return err
 	}
+	wanted := make(map[string]struct{}, len(all))
+	for _, dm := range all {
+		wanted[dm.Domain] = struct{}{}
+	}
+	entries, err := os.ReadDir(m.domDir)
+	if err != nil {
+		return err
+	}
+	for _, entry := range entries {
+		if _, ok := wanted[entry.Name()]; ok {
+			continue
+		}
+		if err := os.RemoveAll(filepath.Join(m.domDir, entry.Name())); err != nil {
+			return err
+		}
+	}
 	for _, dm := range all {
 		if err := m.link(dm.Domain, dm.Username); err != nil {
 			return err
diff --git a/internal/sites/sites_test.go b/internal/sites/sites_test.go
index b408485..7108520 100644
--- a/internal/sites/sites_test.go
+++ b/internal/sites/sites_test.go
@@ -111,6 +111,31 @@ func TestManagerAddRemoveSyncAsk(t *testing.T) {
 	}
 }
 
+func TestSyncRemovesStaleDomainEntries(t *testing.T) {
+	dir := t.TempDir()
+	st, err := store.Open(filepath.Join(dir, "test.db"))
+	if err != nil {
+		t.Fatal(err)
+	}
+	defer st.Close()
+
+	m, err := NewManager(st, dir)
+	if err != nil {
+		t.Fatal(err)
+	}
+	stale := filepath.Join(dir, "domains", "stale.example.com")
+	if err := os.WriteFile(stale, []byte("stale"), 0o644); err != nil {
+		t.Fatal(err)
+	}
+
+	if err := m.Sync(); err != nil {
+		t.Fatal(err)
+	}
+	if _, err := os.Lstat(stale); !os.IsNotExist(err) {
+		t.Errorf("expected stale domain entry removed, got err=%v", err)
+	}
+}
+
 func TestAskUserSubdomain(t *testing.T) {
 	t.Setenv("AGENTBBS_HOST", "bbs.profullstack.com")
 	dir := t.TempDir()