diff --git a/store/store.go b/store/store.go
index 70b95b1e..1e2d5011 100644
--- a/store/store.go
+++ b/store/store.go
@@ -55,6 +55,8 @@ type Store[H header.Header[H]] struct {
 	contiguousHead atomic.Pointer[H]
 	// pending keeps headers pending to be written in one batch
 	pending *batch[H]
+	// syncCh is a channel used to synchronize writes
+	syncCh chan chan struct{}
 
 	Params Parameters
 }
@@ -109,6 +111,7 @@ func newStore[H header.Header[H]](ds datastore.Batching, opts ...Option) (*Store
 		writes:      make(chan []H, 16),
 		writesDn:    make(chan struct{}),
 		pending:     newBatch[H](params.WriteBatchSize),
+		syncCh:      make(chan chan struct{}),
 		Params:      params,
 	}, nil
 }
@@ -153,6 +156,28 @@ func (s *Store[H]) Stop(ctx context.Context) error {
 	return s.metrics.Close()
 }
 
+// Sync ensures all pending writes are synchronized. It blocks until the operation completes or fails.
+func (s *Store[H]) Sync(ctx context.Context) error {
+	waitCh := make(chan struct{})
+	select {
+	case s.syncCh <- waitCh:
+	case <-s.writesDn:
+		return errStoppedStore
+	case <-ctx.Done():
+		return ctx.Err()
+	}
+
+	select {
+	case <-waitCh:
+	case <-s.writesDn:
+		return errStoppedStore
+	case <-ctx.Done():
+		return ctx.Err()
+	}
+
+	return nil
+}
+
 func (s *Store[H]) Height() uint64 {
 	return s.heightSub.Height()
 }
@@ -305,6 +330,12 @@ func (s *Store[H]) HasAt(_ context.Context, height uint64) bool {
 
 // DeleteTo implements [header.Store] interface.
 func (s *Store[H]) DeleteTo(ctx context.Context, to uint64) error {
+	// ensure all the pending headers are synchronized
+	err := s.Sync(ctx)
+	if err != nil {
+		return err
+	}
+
 	head, err := s.Head(ctx)
 	if err != nil {
 		return fmt.Errorf("header/store: reading head: %w", err)
@@ -468,7 +499,8 @@ func (s *Store[H]) Append(ctx context.Context, headers ...H) error {
 func (s *Store[H]) flushLoop() {
 	defer close(s.writesDn)
 	ctx := context.Background()
-	for headers := range s.writes {
+
+	flush := func(headers []H) {
 		s.ensureInit(headers)
 		// add headers to the pending and ensure they are accessible
 		s.pending.Append(headers...)
@@ -482,7 +514,7 @@ func (s *Store[H]) flushLoop() {
 		// don't flush and continue if pending batch is not grown enough,
 		// and Store is not stopping(headers == nil)
 		if s.pending.Len() < s.Params.WriteBatchSize && headers != nil {
-			continue
+			return
 		}
 
 		startTime := time.Now()
@@ -506,15 +538,37 @@ func (s *Store[H]) flushLoop() {
 		s.metrics.flush(ctx, time.Since(startTime), s.pending.Len(), false)
 		// reset pending
 		s.pending.Reset()
+	}
 
-		if headers == nil {
-			// a signal to stop
-			return
+	for {
+		select {
+		case dn := <-s.syncCh:
+			for {
+				select {
+				case headers := <-s.writes:
+					flush(headers)
+					if headers == nil {
+						// a signal to stop
+						return
+					}
+					continue
+				default:
+				}
+
+				close(dn)
+				break
+			}
+		case headers := <-s.writes:
+			flush(headers)
+			if headers == nil {
+				// a signal to stop
+				return
+			}
 		}
 	}
 }
 
-// flush writes the given batch to datastore.
+// flush writes given headers to datastore
 func (s *Store[H]) flush(ctx context.Context, headers ...H) error {
 	ln := len(headers)
 	if ln == 0 {
diff --git a/store/store_test.go b/store/store_test.go
index 0338a539..6a2cf409 100644
--- a/store/store_test.go
+++ b/store/store_test.go
@@ -675,6 +675,32 @@ func TestStore_DeleteTo_MoveHeadAndTail(t *testing.T) {
 	assert.Equal(t, suite.Head().Height(), head.Height())
 }
 
+func TestStore_DeleteTo_Synchronized(t *testing.T) {
+	ctx, cancel := context.WithTimeout(context.Background(), time.Second*5)
+	t.Cleanup(cancel)
+
+	suite := headertest.NewTestSuite(t)
+
+	ds := sync.MutexWrap(datastore.NewMapDatastore())
+	store := NewTestStore(t, ctx, ds, suite.Head(), WithWriteBatchSize(10))
+
+	err := store.Append(ctx, suite.GenDummyHeaders(50)...)
+	require.NoError(t, err)
+
+	err = store.Append(ctx, suite.GenDummyHeaders(50)...)
+	require.NoError(t, err)
+
+	err = store.Append(ctx, suite.GenDummyHeaders(50)...)
+	require.NoError(t, err)
+
+	err = store.DeleteTo(ctx, 100)
+	require.NoError(t, err)
+
+	tail, err := store.Tail(ctx)
+	require.NoError(t, err)
+	require.EqualValues(t, 100, tail.Height())
+}
+
 func TestStorePendingCacheMiss(t *testing.T) {
 	ctx, cancel := context.WithTimeout(context.Background(), time.Second*5)
 	t.Cleanup(cancel)