diff --git a/Code/Framework/AzToolsFramework/AzToolsFramework/Prefab/Instance/Instance.cpp b/Code/Framework/AzToolsFramework/AzToolsFramework/Prefab/Instance/Instance.cpp
index fb7ede42fe..750efa1e36 100644
--- a/Code/Framework/AzToolsFramework/AzToolsFramework/Prefab/Instance/Instance.cpp
+++ b/Code/Framework/AzToolsFramework/AzToolsFramework/Prefab/Instance/Instance.cpp
@@ -237,7 +237,6 @@ namespace AzToolsFramework
 
             if (m_containerEntity)
             {
-                m_instanceEntityMapper->UnregisterEntity(m_containerEntity->GetId());
                 m_containerEntity.reset(aznew AZ::Entity());
                 RegisterEntity(m_containerEntity->GetId(), GenerateEntityAlias());
             }
@@ -265,6 +264,11 @@ namespace AzToolsFramework
 
         void Instance::ClearEntities()
         {
+            if (m_containerEntity)
+            {
+                m_instanceEntityMapper->UnregisterEntity(m_containerEntity->GetId());
+            }
+
             for (const auto&[entityAlias, entity] : m_entities)
             {
                 if (entity)
diff --git a/Code/Framework/AzToolsFramework/AzToolsFramework/Prefab/Instance/InstanceSerializer.cpp b/Code/Framework/AzToolsFramework/AzToolsFramework/Prefab/Instance/InstanceSerializer.cpp
index a2b0f47f57..b5a354ee74 100644
--- a/Code/Framework/AzToolsFramework/AzToolsFramework/Prefab/Instance/InstanceSerializer.cpp
+++ b/Code/Framework/AzToolsFramework/AzToolsFramework/Prefab/Instance/InstanceSerializer.cpp
@@ -168,7 +168,6 @@ namespace AzToolsFramework
 
             if (instance->m_containerEntity)
             {
-                instance->m_instanceEntityMapper->UnregisterEntity(instance->m_containerEntity->GetId());
                 instance->m_containerEntity.reset();
             }