diff --git a/src/node_binding.cc b/src/node_binding.cc
index 80ab4e69e110d0..4dbf56b99a3ddb 100644
--- a/src/node_binding.cc
+++ b/src/node_binding.cc
@@ -1,7 +1,8 @@
 #include "node_binding.h"
-#include "node_errors.h"
 #include <atomic>
 #include "env-inl.h"
+#include "node_errors.h"
+#include "node_external_reference.h"
 #include "node_native_module_env.h"
 #include "util.h"
 
@@ -676,5 +677,13 @@ void RegisterBuiltinModules() {
 #undef V
 }
 
+void RegisterExternalReferences(ExternalReferenceRegistry* registry) {
+  registry->Register(GetLinkedBinding);
+  registry->Register(GetInternalBinding);
+}
+
 }  // namespace binding
 }  // namespace node
+
+NODE_MODULE_EXTERNAL_REFERENCE(binding,
+                               node::binding::RegisterExternalReferences)
diff --git a/src/node_external_reference.h b/src/node_external_reference.h
index 29dd4cb91ed663..8c97eca2264a60 100644
--- a/src/node_external_reference.h
+++ b/src/node_external_reference.h
@@ -46,7 +46,10 @@ class ExternalReferenceRegistry {
   std::vector<intptr_t> external_references_;
 };
 
-#define EXTERNAL_REFERENCE_BINDING_LIST_BASE(V) V(process_object)
+#define EXTERNAL_REFERENCE_BINDING_LIST_BASE(V)                                \
+  V(binding)                                                                   \
+  V(native_module)                                                             \
+  V(process_object)
 
 #define EXTERNAL_REFERENCE_BINDING_LIST(V)                                     \
   EXTERNAL_REFERENCE_BINDING_LIST_BASE(V)
diff --git a/src/node_main_instance.cc b/src/node_main_instance.cc
index 9fefc371d66ab4..617a71e7cac60d 100644
--- a/src/node_main_instance.cc
+++ b/src/node_main_instance.cc
@@ -259,10 +259,17 @@ NodeMainInstance::CreateMainEnvironment(int* exit_code,
   env->InitializeInspector({});
 #endif
 
-  if (env->RunBootstrapping().IsEmpty()) {
+  if (!deserialize_mode_ && env->RunBootstrapping().IsEmpty()) {
     return nullptr;
   }
 
+  if (deserialize_mode_ && env->BootstrapNode().IsEmpty()) {
+    return nullptr;
+  }
+
+  CHECK(env->req_wrap_queue()->IsEmpty());
+  CHECK(env->handle_wrap_queue()->IsEmpty());
+  env->set_has_run_bootstrapping_code(true);
   return env;
 }
 
diff --git a/src/node_native_module_env.cc b/src/node_native_module_env.cc
index e38529eefae9c4..b59ed7cb75cf67 100644
--- a/src/node_native_module_env.cc
+++ b/src/node_native_module_env.cc
@@ -1,5 +1,6 @@
 #include "node_native_module_env.h"
 #include "env-inl.h"
+#include "node_external_reference.h"
 
 namespace node {
 namespace native_module {
@@ -216,8 +217,21 @@ void NativeModuleEnv::Initialize(Local<Object> target,
   target->SetIntegrityLevel(context, IntegrityLevel::kFrozen).FromJust();
 }
 
+void NativeModuleEnv::RegisterExternalReferences(
+    ExternalReferenceRegistry* registry) {
+  registry->Register(ConfigStringGetter);
+  registry->Register(ModuleIdsGetter);
+  registry->Register(GetModuleCategories);
+  registry->Register(GetCacheUsage);
+  registry->Register(CompileFunction);
+  registry->Register(HasCachedBuiltins);
+}
+
 }  // namespace native_module
 }  // namespace node
 
 NODE_MODULE_CONTEXT_AWARE_INTERNAL(
     native_module, node::native_module::NativeModuleEnv::Initialize)
+NODE_MODULE_EXTERNAL_REFERENCE(
+    native_module,
+    node::native_module::NativeModuleEnv::RegisterExternalReferences)
diff --git a/src/node_native_module_env.h b/src/node_native_module_env.h
index bc36be75109639..0a53771ff5d1ca 100644
--- a/src/node_native_module_env.h
+++ b/src/node_native_module_env.h
@@ -7,6 +7,7 @@
 
 namespace node {
 class Environment;
+class ExternalReferenceRegistry;
 
 namespace native_module {
 
@@ -14,6 +15,7 @@ extern const bool has_code_cache;
 
 class NativeModuleEnv {
  public:
+  static void RegisterExternalReferences(ExternalReferenceRegistry* registry);
   static void Initialize(v8::Local<v8::Object> target,
                          v8::Local<v8::Value> unused,
                          v8::Local<v8::Context> context,
diff --git a/tools/snapshot/snapshot_builder.cc b/tools/snapshot/snapshot_builder.cc
index 7086a98a6c80c8..364202711105a4 100644
--- a/tools/snapshot/snapshot_builder.cc
+++ b/tools/snapshot/snapshot_builder.cc
@@ -130,6 +130,7 @@ std::string SnapshotBuilder::Generate(
                             nullptr,
                             node::EnvironmentFlags::kDefaultFlags,
                             {});
+      env->BootstrapInternalLoaders().ToLocalChecked();
       if (per_process::enabled_debug_list.enabled(DebugCategory::MKSNAPSHOT)) {
         env->PrintAllBaseObjects();
         printf("Environment = %p\n", env);