diff --git a/modules/fbx/fbx_document.cpp b/modules/fbx/fbx_document.cpp
index bde23289f474..44a929d285d3 100644
--- a/modules/fbx/fbx_document.cpp
+++ b/modules/fbx/fbx_document.cpp
@@ -1629,6 +1629,9 @@ void FBXDocument::_generate_skeleton_bone_node(Ref<FBXState> p_state, const GLTF
 
 	active_skeleton = skeleton;
 	current_node = active_skeleton;
+	if (active_skeleton) {
+		p_scene_parent = active_skeleton;
+	}
 
 	if (requires_extra_node) {
 		current_node = nullptr;
@@ -2019,8 +2022,8 @@ Node *FBXDocument::generate_scene(Ref<GLTFState> p_state, float p_bake_fps, bool
 	GLTFNodeIndex fbx_root = state->root_nodes.write[0];
 	Node *fbx_root_node = state->get_scene_node(fbx_root);
 	Node *root = fbx_root_node;
-	if (fbx_root_node && fbx_root_node->get_parent()) {
-		root = fbx_root_node->get_parent();
+	if (root && root->get_owner() && root->get_owner() != root) {
+		root = root->get_owner();
 	}
 	ERR_FAIL_NULL_V(root, nullptr);
 	_process_mesh_instances(state, root);
diff --git a/modules/gltf/gltf_document.cpp b/modules/gltf/gltf_document.cpp
index f8c35ab6d1f7..8f0f0d219efb 100644
--- a/modules/gltf/gltf_document.cpp
+++ b/modules/gltf/gltf_document.cpp
@@ -5685,6 +5685,9 @@ void GLTFDocument::_generate_skeleton_bone_node(Ref<GLTFState> p_state, const GL
 
 	active_skeleton = skeleton;
 	current_node = active_skeleton;
+	if (active_skeleton) {
+		p_scene_parent = active_skeleton;
+	}
 
 	if (requires_extra_node) {
 		current_node = nullptr;
@@ -7104,6 +7107,9 @@ Node *GLTFDocument::_generate_scene_node_tree(Ref<GLTFState> p_state) {
 	if (p_state->extensions_used.has("GODOT_single_root")) {
 		_generate_scene_node(p_state, 0, nullptr, nullptr);
 		single_root = p_state->scene_nodes[0];
+		if (single_root && single_root->get_owner() && single_root->get_owner() != single_root) {
+			single_root = single_root->get_owner();
+		}
 	} else {
 		single_root = memnew(Node3D);
 		for (int32_t root_i = 0; root_i < p_state->root_nodes.size(); root_i++) {