diff --git a/Source/Engine/Level/Prefabs/Prefab.Apply.cpp b/Source/Engine/Level/Prefabs/Prefab.Apply.cpp
index a5abf2221..53453afe9 100644
--- a/Source/Engine/Level/Prefabs/Prefab.Apply.cpp
+++ b/Source/Engine/Level/Prefabs/Prefab.Apply.cpp
@@ -336,7 +336,7 @@ bool PrefabInstanceData::SynchronizePrefabInstances(PrefabInstancesData& prefabI
                 continue;
             }
 
-            SceneObject* obj = SceneObjectsFactory::Spawn(context, *(ISerializable::DeserializeStream*)data);
+            SceneObject* obj = SceneObjectsFactory::Spawn(context, *data);
             if (!obj)
                 continue;
             obj->RegisterObject();
diff --git a/Source/Engine/Level/Prefabs/Prefab.cpp b/Source/Engine/Level/Prefabs/Prefab.cpp
index 9c1060c0f..c2c2463b2 100644
--- a/Source/Engine/Level/Prefabs/Prefab.cpp
+++ b/Source/Engine/Level/Prefabs/Prefab.cpp
@@ -2,6 +2,7 @@
 
 #include "Prefab.h"
 #include "Engine/Serialization/JsonTools.h"
+#include "Engine/Content/Content.h"
 #include "Engine/Content/Factories/JsonAssetFactory.h"
 #include "Engine/Core/Log.h"
 #include "Engine/Level/Prefabs/PrefabManager.h"
@@ -21,6 +22,36 @@ Prefab::Prefab(const SpawnParams& params, const AssetInfo* info)
 {
 }
 
+Guid Prefab::GetRootObjectId() const
+{
+    ASSERT(IsLoaded());
+    ScopeLock lock(Locker);
+
+    // Root is always the first but handle case when prefab root was reordered in the base prefab while the nested prefab has still the old state
+    // TODO: resave and force sync prefabs during game cooking so this step could be skipped in game
+    int32 objectIndex = 0;
+    if (NestedPrefabs.HasItems())
+    {
+        const auto& data = *Data;
+        const Guid basePrefabId = JsonTools::GetGuid(data[objectIndex], "PrefabID");
+        if (const auto basePrefab = Content::Load<Prefab>(basePrefabId))
+        {
+            const Guid basePrefabRootId = basePrefab->GetRootObjectId();
+            for (int32 i = 0; i < ObjectsCount; i++)
+            {
+                const Guid prefabObjectId = JsonTools::GetGuid(data[i], "PrefabObjectID");
+                if (prefabObjectId == basePrefabRootId)
+                {
+                    objectIndex = i;
+                    break;   
+                }
+            }
+        }
+    }
+
+    return ObjectsIds[objectIndex];
+}
+
 Actor* Prefab::GetDefaultInstance()
 {
     ScopeLock lock(Locker);
diff --git a/Source/Engine/Level/Prefabs/Prefab.h b/Source/Engine/Level/Prefabs/Prefab.h
index ed82473c9..5e0075edf 100644
--- a/Source/Engine/Level/Prefabs/Prefab.h
+++ b/Source/Engine/Level/Prefabs/Prefab.h
@@ -50,11 +50,7 @@ public:
     /// <summary>
     /// Gets the root object identifier (prefab object ID). Asset must be loaded.
     /// </summary>
-    Guid GetRootObjectId() const
-    {
-        ASSERT(IsLoaded());
-        return ObjectsIds[0];
-    }
+    Guid GetRootObjectId() const;
 
     /// <summary>
     /// Requests the default prefab object instance. Deserializes the prefab objects from the asset. Skips if already done.
diff --git a/Source/Engine/Level/Prefabs/PrefabManager.cpp b/Source/Engine/Level/Prefabs/PrefabManager.cpp
index cc42967a4..88d80a41a 100644
--- a/Source/Engine/Level/Prefabs/PrefabManager.cpp
+++ b/Source/Engine/Level/Prefabs/PrefabManager.cpp
@@ -121,7 +121,7 @@ Actor* PrefabManager::SpawnPrefab(Prefab* prefab, Actor* parent, Dictionary<Guid
     for (int32 i = 0; i < objectsCount; i++)
     {
         auto& stream = data[i];
-        auto obj = SceneObjectsFactory::Spawn(context, stream);
+        SceneObject* obj = SceneObjectsFactory::Spawn(context, stream);
         sceneObjects->At(i) = obj;
         if (obj)
             obj->RegisterObject();
@@ -146,16 +146,25 @@ Actor* PrefabManager::SpawnPrefab(Prefab* prefab, Actor* parent, Dictionary<Guid
     }
     Scripting::ObjectsLookupIdMapping.Set(prevIdMapping);
 
-    // Assume that prefab has always only one root actor that is serialized first
-    if (sceneObjects.Value->IsEmpty())
+    // Pick prefab root object
+    if (sceneObjects->IsEmpty())
     {
         LOG(Warning, "No valid objects in prefab.");
         return nullptr;
     }
-    auto root = (Actor*)sceneObjects.Value->At(0);
+    Actor* root = nullptr;
+    const Guid prefabRootObjectId = prefab->GetRootObjectId();
+    for (int32 i = 0; i < objectsCount; i++)
+    {
+        if (JsonTools::GetGuid(data[i], "ID") == prefabRootObjectId)
+        {
+            root = dynamic_cast<Actor*>(sceneObjects->At(i));
+            break;
+        }
+    }
     if (!root)
     {
-        LOG(Warning, "Failed to load prefab root object.");
+        LOG(Warning, "Missing prefab root object.");
         return nullptr;
     }
 
@@ -167,6 +176,8 @@ Actor* PrefabManager::SpawnPrefab(Prefab* prefab, Actor* parent, Dictionary<Guid
     }
 
     // Prepare parent linkage for prefab root actor
+    if (root->_parent)
+        root->_parent->Children.Remove(root);
     root->_parent = parent;
     if (parent)
         parent->Children.Add(root);
@@ -174,16 +185,16 @@ Actor* PrefabManager::SpawnPrefab(Prefab* prefab, Actor* parent, Dictionary<Guid
     // Link actors hierarchy
     for (int32 i = 0; i < sceneObjects->Count(); i++)
     {
-        auto obj = sceneObjects->At(i);
+        SceneObject* obj = sceneObjects->At(i);
         if (obj)
             obj->Initialize();
     }
 
     // Delete objects without parent or with invalid linkage to the prefab
-    for (int32 i = 1; i < sceneObjects->Count(); i++)
+    for (int32 i = 0; i < sceneObjects->Count(); i++)
     {
         SceneObject* obj = sceneObjects->At(i);
-        if (!obj)
+        if (!obj || obj == root)
             continue;
 
         // Check for missing parent (eg. parent object has been deleted)
@@ -251,8 +262,7 @@ Actor* PrefabManager::SpawnPrefab(Prefab* prefab, Actor* parent, Dictionary<Guid
         const Guid prefabObjectId = JsonTools::GetGuid(stream, "ID");
         if (objectsCache)
             objectsCache->Add(prefabObjectId, obj);
-        obj->_prefabID = prefabId;
-        obj->_prefabObjectID = prefabObjectId;
+        obj->LinkPrefab(prefabId, prefabObjectId);
     }
 
     // Update transformations
@@ -317,7 +327,7 @@ bool PrefabManager::CreatePrefab(Actor* targetActor, const StringView& outputPat
         writer.StartArray();
         for (int32 i = 0; i < sceneObjects->Count(); i++)
         {
-            SceneObject* obj = sceneObjects.Value->At(i);
+            SceneObject* obj = sceneObjects->At(i);
             writer.SceneObject(obj);
         }
         writer.EndArray();
@@ -335,7 +345,7 @@ bool PrefabManager::CreatePrefab(Actor* targetActor, const StringView& outputPat
     for (int32 i = 0; i < sceneObjects->Count(); i++)
     {
         // Generate new IDs for the prefab objects (other than reference instance used to create prefab)
-        const SceneObject* obj = sceneObjects.Value->At(i);
+        const SceneObject* obj = sceneObjects->At(i);
         objectInstanceIdToPrefabObjectId.Add(obj->GetSceneObjectId(), Guid::New());
     }
     {
@@ -382,7 +392,7 @@ bool PrefabManager::CreatePrefab(Actor* targetActor, const StringView& outputPat
 
         for (int32 i = 0; i < sceneObjects->Count(); i++)
         {
-            SceneObject* obj = sceneObjects.Value->At(i);
+            SceneObject* obj = sceneObjects->At(i);
             Guid prefabObjectId;
 
             if (objectInstanceIdToPrefabObjectId.TryGet(obj->GetSceneObjectId(), prefabObjectId))
diff --git a/Source/Engine/Level/SceneObject.h b/Source/Engine/Level/SceneObject.h
index 0425a3a76..64bda4a59 100644
--- a/Source/Engine/Level/SceneObject.h
+++ b/Source/Engine/Level/SceneObject.h
@@ -58,6 +58,7 @@ API_CLASS(Abstract, NoSpawn) class FLAXENGINE_API SceneObject : public Scripting
 {
     DECLARE_SCRIPTING_TYPE_NO_SPAWN(SceneObject);
     friend PrefabInstanceData;
+    friend PrefabManager;
     friend Actor;
     friend Level;
     friend ScriptsFactory;
diff --git a/Source/Engine/Level/SceneObjectsFactory.cpp b/Source/Engine/Level/SceneObjectsFactory.cpp
index 35629dc6a..00fd29be0 100644
--- a/Source/Engine/Level/SceneObjectsFactory.cpp
+++ b/Source/Engine/Level/SceneObjectsFactory.cpp
@@ -31,7 +31,7 @@ void SceneObjectsFactory::Context::SetupIdsMapping(const SceneObject* obj)
     }
 }
 
-SceneObject* SceneObjectsFactory::Spawn(Context& context, ISerializable::DeserializeStream& stream)
+SceneObject* SceneObjectsFactory::Spawn(Context& context, const ISerializable::DeserializeStream& stream)
 {
     // Get object id
     Guid id = JsonTools::GetGuid(stream, "ID");
@@ -81,7 +81,7 @@ SceneObject* SceneObjectsFactory::Spawn(Context& context, ISerializable::Deseria
         context.Modifier->IdsMapping[prefabObjectId] = id;
 
         // Create prefab instance (recursive prefab loading to support nested prefabs)
-        obj = Spawn(context, *(ISerializable::DeserializeStream*)prefabData);
+        obj = Spawn(context, *prefabData);
     }
     else
     {
@@ -584,7 +584,7 @@ void SceneObjectsFactory::SynchronizeNewPrefabInstance(Context& context, PrefabS
     data.Modifier->IdsMapping[prefabObjectId] = id;
 
     // Create prefab instance (recursive prefab loading to support nested prefabs)
-    auto child = Spawn(context, *(ISerializable::DeserializeStream*)prefabData);
+    auto child = Spawn(context, *prefabData);
     if (!child)
     {
         LOG(Warning, "Failed to create object {1} from prefab {0}.", prefab->ToString(), prefabObjectId);
diff --git a/Source/Engine/Level/SceneObjectsFactory.h b/Source/Engine/Level/SceneObjectsFactory.h
index 1534b7359..d3f5b3dd7 100644
--- a/Source/Engine/Level/SceneObjectsFactory.h
+++ b/Source/Engine/Level/SceneObjectsFactory.h
@@ -35,7 +35,7 @@ public:
     /// </summary>
     /// <param name="context">The serialization context.</param>
     /// <param name="stream">The serialized data stream.</param>
-    static SceneObject* Spawn(Context& context, ISerializable::DeserializeStream& stream);
+    static SceneObject* Spawn(Context& context, const ISerializable::DeserializeStream& stream);
 
     /// <summary>
     /// Deserializes the scene object from the specified data value.