diff --git a/internal/state/store.go b/internal/state/store.go
index d2a3c54..f9912a3 100644
--- a/internal/state/store.go
+++ b/internal/state/store.go
@@ -3,9 +3,11 @@ package state
 
 import (
 	"encoding/json"
+	"errors"
 	"fmt"
 	"os"
 	"path/filepath"
+	"syscall"
 
 	"github.com/Neokil/AutoPR/internal/domain/workflowstate"
 	"github.com/Neokil/AutoPR/internal/gitutil"
@@ -72,7 +74,10 @@ func (s *Store) SaveState(ticketNumber string, state workflowstate.State) error
 			return fmt.Errorf("write worktree state: %w", err)
 		}
 		// Remove the pre-worktree copy so there is only one source of truth.
-		_ = os.Remove(filepath.Join(s.TicketDir(ticketNumber), StateFileName))
+		err = s.cleanupLegacyTicketDir(ticketNumber)
+		if err != nil {
+			return err
+		}
 
 		return nil
 	}
@@ -160,6 +165,24 @@ func (s *Store) ensureTicketDir(ticketNumber string) (string, error) {
 	return dir, nil
 }
 
+func (s *Store) cleanupLegacyTicketDir(ticketNumber string) error {
+	statePath := filepath.Join(s.TicketDir(ticketNumber), StateFileName)
+	err := os.Remove(statePath)
+	if err != nil && !os.IsNotExist(err) {
+		return fmt.Errorf("remove legacy state file: %w", err)
+	}
+
+	err = os.Remove(s.TicketDir(ticketNumber))
+	if err == nil || os.IsNotExist(err) {
+		return nil
+	}
+	if errors.Is(err, syscall.ENOTEMPTY) {
+		return nil
+	}
+
+	return fmt.Errorf("remove legacy ticket dir: %w", err)
+}
+
 func parseStateJSON(_ string, data []byte) (workflowstate.State, error) {
 	var state workflowstate.State
 	err := json.Unmarshal(data, &state)
diff --git a/internal/state/store_test.go b/internal/state/store_test.go
new file mode 100644
index 0000000..522da8d
--- /dev/null
+++ b/internal/state/store_test.go
@@ -0,0 +1,123 @@
+package state_test
+
+import (
+	"os"
+	"path/filepath"
+	"slices"
+	"testing"
+
+	workflowstate "github.com/Neokil/AutoPR/internal/domain/workflowstate"
+	"github.com/Neokil/AutoPR/internal/state"
+)
+
+func TestSaveStateCreatesPreWorktreeStateFile(t *testing.T) {
+	t.Parallel()
+
+	repoRoot := t.TempDir()
+	store := state.NewStore(repoRoot, ".auto-pr-state")
+	ticketState := workflowstate.New("GH-12")
+
+	err := store.SaveState(ticketState.TicketNumber, ticketState)
+	if err != nil {
+		t.Fatalf("SaveState() error = %v", err)
+	}
+
+	statePath := filepath.Join(store.TicketDir(ticketState.TicketNumber), state.StateFileName)
+	_, statErr := os.Stat(statePath)
+	if statErr != nil {
+		t.Fatalf("expected pre-worktree state file at %s: %v", statePath, statErr)
+	}
+}
+
+func TestSaveStateMigratesStateAndRemovesEmptyLegacyDir(t *testing.T) {
+	t.Parallel()
+
+	repoRoot := t.TempDir()
+	store := state.NewStore(repoRoot, ".auto-pr-state")
+	ticketState := workflowstate.New("GH-12")
+
+	err := store.SaveState(ticketState.TicketNumber, ticketState)
+	if err != nil {
+		t.Fatalf("initial SaveState() error = %v", err)
+	}
+
+	ticketState.WorktreePath = filepath.Join(repoRoot, ".auto-pr-state", "worktrees", ticketState.TicketNumber)
+	err = store.SaveState(ticketState.TicketNumber, ticketState)
+	if err != nil {
+		t.Fatalf("migrating SaveState() error = %v", err)
+	}
+
+	worktreeStatePath := filepath.Join(ticketState.WorktreePath, ".auto-pr", state.StateFileName)
+	_, worktreeStateErr := os.Stat(worktreeStatePath)
+	if worktreeStateErr != nil {
+		t.Fatalf("expected worktree state file at %s: %v", worktreeStatePath, worktreeStateErr)
+	}
+
+	legacyStatePath := filepath.Join(store.TicketDir(ticketState.TicketNumber), state.StateFileName)
+	_, legacyStateErr := os.Stat(legacyStatePath)
+	if !os.IsNotExist(legacyStateErr) {
+		t.Fatalf("expected legacy state file to be removed, got err=%v", legacyStateErr)
+	}
+
+	_, legacyDirErr := os.Stat(store.TicketDir(ticketState.TicketNumber))
+	if !os.IsNotExist(legacyDirErr) {
+		t.Fatalf("expected empty legacy ticket dir to be removed, got err=%v", legacyDirErr)
+	}
+}
+
+func TestSaveStateKeepsLegacyDirWhenItContainsOtherFiles(t *testing.T) {
+	t.Parallel()
+
+	repoRoot := t.TempDir()
+	store := state.NewStore(repoRoot, ".auto-pr-state")
+	ticketState := workflowstate.New("GH-12")
+
+	err := store.SaveState(ticketState.TicketNumber, ticketState)
+	if err != nil {
+		t.Fatalf("initial SaveState() error = %v", err)
+	}
+
+	notePath := filepath.Join(store.TicketDir(ticketState.TicketNumber), "note.txt")
+	err = os.WriteFile(notePath, []byte("keep me\n"), 0o644)
+	if err != nil {
+		t.Fatalf("WriteFile() error = %v", err)
+	}
+
+	ticketState.WorktreePath = filepath.Join(repoRoot, ".auto-pr-state", "worktrees", ticketState.TicketNumber)
+	err = store.SaveState(ticketState.TicketNumber, ticketState)
+	if err != nil {
+		t.Fatalf("migrating SaveState() error = %v", err)
+	}
+
+	_, noteStatErr := os.Stat(notePath)
+	if noteStatErr != nil {
+		t.Fatalf("expected extra file to remain in legacy dir: %v", noteStatErr)
+	}
+}
+
+func TestListTicketDirsIncludesMigratedWorktreeState(t *testing.T) {
+	t.Parallel()
+
+	repoRoot := t.TempDir()
+	store := state.NewStore(repoRoot, ".auto-pr-state")
+	ticketState := workflowstate.New("GH-12")
+
+	err := store.SaveState(ticketState.TicketNumber, ticketState)
+	if err != nil {
+		t.Fatalf("initial SaveState() error = %v", err)
+	}
+
+	ticketState.WorktreePath = filepath.Join(repoRoot, ".auto-pr-state", "worktrees", ticketState.TicketNumber)
+	err = store.SaveState(ticketState.TicketNumber, ticketState)
+	if err != nil {
+		t.Fatalf("migrating SaveState() error = %v", err)
+	}
+
+	tickets, err := store.ListTicketDirs()
+	if err != nil {
+		t.Fatalf("ListTicketDirs() error = %v", err)
+	}
+	if !slices.Contains(tickets, ticketState.TicketNumber) {
+		t.Fatalf("expected migrated ticket %q in %v", ticketState.TicketNumber, tickets)
+	}
+}