diff --git a/Code/Framework/AzToolsFramework/AzToolsFramework/Prefab/Instance/InstanceSerializer.cpp b/Code/Framework/AzToolsFramework/AzToolsFramework/Prefab/Instance/InstanceSerializer.cpp
index b5a354ee74..92b37b10db 100644
--- a/Code/Framework/AzToolsFramework/AzToolsFramework/Prefab/Instance/InstanceSerializer.cpp
+++ b/Code/Framework/AzToolsFramework/AzToolsFramework/Prefab/Instance/InstanceSerializer.cpp
@@ -15,6 +15,7 @@
 #include <AzToolsFramework/Prefab/Instance/InstanceEntityMapperInterface.h>
 #include <AzToolsFramework/Prefab/PrefabLoaderInterface.h>
 #include <AzToolsFramework/Prefab/PrefabSystemComponentInterface.h>
+#include <Prefab/PrefabDomUtils.h>
 
 namespace AzToolsFramework
 {
@@ -81,6 +82,15 @@ namespace AzToolsFramework
                 result.Combine(resultInstances);
             }
 
+            PrefabDomUtils::LinkIdMetadata* subPathLinkId = context.GetMetadata().Find<PrefabDomUtils::LinkIdMetadata>();
+            if (subPathLinkId)
+            {
+                AZ::ScopedContextPath subPathSource(context, "m_linkId");
+
+                result = ContinueStoringToJsonObjectField(
+                    outputValue, "LinkId", &(instance->m_linkId), &InvalidLinkId, azrtti_typeid<decltype(instance->m_linkId)>(), context);
+            }
+
             return context.Report(result,
                 result.GetProcessing() == JSR::Processing::Completed ? "Successfully stored Instance information for Prefab." :
                 "Failed to store Instance information for Prefab.");
diff --git a/Code/Framework/AzToolsFramework/AzToolsFramework/Prefab/PrefabDomUtils.cpp b/Code/Framework/AzToolsFramework/AzToolsFramework/Prefab/PrefabDomUtils.cpp
index 1ad88e53d2..dcc14d3b91 100644
--- a/Code/Framework/AzToolsFramework/AzToolsFramework/Prefab/PrefabDomUtils.cpp
+++ b/Code/Framework/AzToolsFramework/AzToolsFramework/Prefab/PrefabDomUtils.cpp
@@ -88,6 +88,11 @@ namespace AzToolsFramework
                     settings.m_keepDefaults = true;
                 }
 
+                if ((flags & StoreFlags::StoreLinkIds) != StoreFlags::None)
+                {
+                    settings.m_metadata.Create<LinkIdMetadata>();
+                }
+
                 AZStd::string scratchBuffer;
                 auto issueReportingCallback = [&scratchBuffer]
                 (AZStd::string_view message, AZ::JsonSerializationResult::ResultCode result,
diff --git a/Code/Framework/AzToolsFramework/AzToolsFramework/Prefab/PrefabDomUtils.h b/Code/Framework/AzToolsFramework/AzToolsFramework/Prefab/PrefabDomUtils.h
index b04cf9f57d..7cab24ad9f 100644
--- a/Code/Framework/AzToolsFramework/AzToolsFramework/Prefab/PrefabDomUtils.h
+++ b/Code/Framework/AzToolsFramework/AzToolsFramework/Prefab/PrefabDomUtils.h
@@ -45,7 +45,11 @@ namespace AzToolsFramework
 
                 //! By default an instance will be stored with default values. In cases where we want to store less json without defaults
                 //! such as saving to disk, this flag will control that behavior.
-                StripDefaultValues = 1 << 0
+                StripDefaultValues = 1 << 0,
+
+                //! We do not save linkIds to file. However when loading a level we want to temporarily save
+                //! linkIds to instance dom so any nested prefabs will have linkIds correctly set.
+                StoreLinkIds = 1 << 1
             };
             AZ_DEFINE_ENUM_BITWISE_OPERATORS(StoreFlags);
 
@@ -150,6 +154,14 @@ namespace AzToolsFramework
                 [[maybe_unused]] const AZStd::string_view printMessage,
                 [[maybe_unused]] const AzToolsFramework::Prefab::PrefabDomValue& prefabDomValue);
 
+            //! An empty struct for passing to JsonSerializerSettings.m_metadata that is consumed by InstanceSerializer::Store.
+            //! If present in metadata, linkIds will be stored to instance dom.
+            struct LinkIdMetadata
+            {
+                AZ_RTTI(LinkIdMetadata, "{8FF7D299-14E3-41D4-90C5-393A240FAE7C}");
+
+                virtual ~LinkIdMetadata() {}
+            };
         } // namespace PrefabDomUtils
     } // namespace Prefab
 } // namespace AzToolsFramework
diff --git a/Code/Framework/AzToolsFramework/AzToolsFramework/Prefab/PrefabLoader.cpp b/Code/Framework/AzToolsFramework/AzToolsFramework/Prefab/PrefabLoader.cpp
index 5091a2d1bc..0a9c937832 100644
--- a/Code/Framework/AzToolsFramework/AzToolsFramework/Prefab/PrefabLoader.cpp
+++ b/Code/Framework/AzToolsFramework/AzToolsFramework/Prefab/PrefabLoader.cpp
@@ -300,7 +300,7 @@ namespace AzToolsFramework
             }
 
             PrefabDom storedPrefabDom(&loadedTemplateDom->get().GetAllocator());
-            if (!PrefabDomUtils::StoreInstanceInPrefabDom(loadedPrefabInstance, storedPrefabDom))
+            if (!PrefabDomUtils::StoreInstanceInPrefabDom(loadedPrefabInstance, storedPrefabDom, PrefabDomUtils::StoreFlags::StoreLinkIds))
             {
                 return false;
             }