diff --git a/pkg/local_object_storage/pilorama/boltdb.go b/pkg/local_object_storage/pilorama/boltdb.go
index 901bfd58e..044c3fc6d 100644
--- a/pkg/local_object_storage/pilorama/boltdb.go
+++ b/pkg/local_object_storage/pilorama/boltdb.go
@@ -1128,7 +1128,7 @@ func (t *boltForest) TreeSortedByFilename(ctx context.Context, cid cidSDK.ID, tr
 		}
 
 		t.fillSortedChildren(b, nodeIDs, h)
-
+		h.mergeByFilename()
 		for info, ok := h.pop(); ok; info, ok = h.pop() {
 			for _, id := range info.id {
 				childInfo, err := t.getChildInfo(b, key, id)
@@ -1155,7 +1155,7 @@ func (t *boltForest) TreeSortedByFilename(ctx context.Context, cid cidSDK.ID, tr
 	}
 	if len(res) != 0 {
 		s := string(findAttr(res[len(res)-1].Meta, AttributeFilename))
-		cursor = &Cursor{Filename: s}
+		cursor = &Cursor{Filename: s, Node: &res[len(res)-1].Children[len(res[len(res)-1].Children)-1]}
 	}
 	return res, cursor, metaerr.Wrap(err)
 }
diff --git a/pkg/local_object_storage/pilorama/heap.go b/pkg/local_object_storage/pilorama/heap.go
index c59a02b09..3ba5265b7 100644
--- a/pkg/local_object_storage/pilorama/heap.go
+++ b/pkg/local_object_storage/pilorama/heap.go
@@ -53,6 +53,25 @@ func (h *fixedHeap) push(id MultiNode, filename string) bool {
 	if h.start != nil && filename <= (*h.start).Filename {
 		return false
 	}
+	slices.Sort(id)
+
+	if h.start != nil {
+		if filename < (*h.start).Filename {
+			return false
+		} else if filename == (*h.start).Filename {
+			if (*h.start).Node == nil {
+				return false
+			}
+			// A tree may have a lot of nodes with the same filename but different versions so that
+			// len(nodes) > batch_size. The cut nodes should be pushed into the result on repeated call
+			// with the same filename.
+			pos, found := slices.BinarySearch(id, *(*h.start).Node)
+			if !found || pos+1 >= len(id) {
+				return false
+			}
+			id = id[pos+1:]
+		}
+	}
 
 	*h.h = append(*h.h, heapInfo{id: id, filename: filename})
 	h.sorted = false
@@ -66,6 +85,38 @@ func (h *fixedHeap) push(id MultiNode, filename string) bool {
 	return true
 }
 
+// mergeByFilename merges heap entries with identical filenames by combining their IDs.
+// Identical filenames may appear in the heap after few pushes for example by `fillSortedChildren` method:
+//
+// heap entry 1: {filename: "somefilenameB", id: [33, 45]}
+// heap entry 2: {filename: "somefilenameA", id: [13, 15, 40]}
+// heap entry 3: {filename: "somefilenameB", id: [1, 14, 29]}
+//
+// After merge we get:
+//
+// heap entry 1: {filename: "somefilenameB", id: [1, 14, 29, 33, 45]}
+// heap entry 2: {filename: "somefilenameA", id: [13, 15, 40]}.
+func (h *fixedHeap) mergeByFilename() {
+	m := make(map[string]MultiNode)
+
+	for _, heapInfo := range *h.h {
+		m[heapInfo.filename] = append(m[heapInfo.filename], heapInfo.id...)
+	}
+
+	newHeap := make([]heapInfo, 0, len(m))
+
+	for filename, ids := range m {
+		slices.Sort(ids)
+
+		newHeap = append(newHeap, heapInfo{
+			filename: filename,
+			id:       ids,
+		})
+	}
+
+	*h.h = newHeap
+}
+
 func (h *fixedHeap) pop() (heapInfo, bool) {
 	if !h.sorted {
 		slices.SortFunc(*h.h, func(a, b heapInfo) int {
diff --git a/pkg/local_object_storage/pilorama/interface.go b/pkg/local_object_storage/pilorama/interface.go
index b7694ab7c..641ab6ef3 100644
--- a/pkg/local_object_storage/pilorama/interface.go
+++ b/pkg/local_object_storage/pilorama/interface.go
@@ -85,6 +85,9 @@ const (
 type Cursor struct {
 	// Last traversed filename.
 	Filename string
+
+	// Last traversed node.
+	Node *Node
 }
 
 // CIDDescriptor contains container ID and information about the node position
diff --git a/pkg/services/tree/service.go b/pkg/services/tree/service.go
index ef0a38bc1..19c577f8a 100644
--- a/pkg/services/tree/service.go
+++ b/pkg/services/tree/service.go
@@ -467,7 +467,7 @@ func getSortedSubTree(ctx context.Context, srv TreeService_GetSubTreeServer, cid
 			item.values = nodes
 			item.cursor = cursor
 
-			if len(nodes) == 0 {
+			if len(item.values) == 0 {
 				stack = stack[:len(stack)-1]
 				continue
 			}