diff --git a/Assets/VRM/Editor/Format/VRMEditorImporterContext.cs b/Assets/VRM/Editor/Format/VRMEditorImporterContext.cs
index f29d76f10..ae0946d36 100644
--- a/Assets/VRM/Editor/Format/VRMEditorImporterContext.cs
+++ b/Assets/VRM/Editor/Format/VRMEditorImporterContext.cs
@@ -141,6 +141,9 @@ namespace VRM
             loaded.TransferOwnership(SaveAsAsset);
             var root = loaded.Root;
 
+            // Remove RuntimeGltfInstance component before saving as a prefab.
+            UnityObjectDestoyer.DestroyRuntimeOrEditor(loaded);
+
             // Create or update Main Asset
             if (m_prefabPath.IsFileExists)
             {
@@ -155,7 +158,7 @@ namespace VRM
             }
 
             // destroy GameObject on scene
-            GameObject.DestroyImmediate(root);
+            UnityObjectDestoyer.DestroyRuntimeOrEditor(root);
 
             foreach (var x in m_paths)
             {