diff --git a/lib/internal/bootstrap/node.js b/lib/internal/bootstrap/node.js
index 2bafb2a3ad3595..50f5001aa4b0fd 100644
--- a/lib/internal/bootstrap/node.js
+++ b/lib/internal/bootstrap/node.js
@@ -210,17 +210,6 @@ function startup() {
       'DeprecationWarning', 'DEP0062', startup, true);
   }
 
-  const experimentalModules = getOptionValue('--experimental-modules');
-  const experimentalVMModules = getOptionValue('--experimental-vm-modules');
-  if (experimentalModules || experimentalVMModules) {
-    if (experimentalModules) {
-      process.emitWarning(
-        'The ESM module loader is experimental.',
-        'ExperimentalWarning', undefined);
-    }
-    NativeModule.require('internal/process/esm_loader').setup();
-  }
-
   const { deprecate } = NativeModule.require('internal/util');
   {
     // Install legacy getters on the `util` binding for typechecking.
@@ -451,6 +440,30 @@ function prepareUserCodeExecution() {
     delete process.env.NODE_UNIQUE_ID;
   }
 
+  const experimentalModules = getOptionValue('--experimental-modules');
+  const experimentalVMModules = getOptionValue('--experimental-vm-modules');
+  if (experimentalModules || experimentalVMModules) {
+    if (experimentalModules) {
+      process.emitWarning(
+        'The ESM module loader is experimental.',
+        'ExperimentalWarning', undefined);
+    }
+
+    const {
+      setImportModuleDynamicallyCallback,
+      setInitializeImportMetaObjectCallback
+    } = internalBinding('module_wrap');
+    const esm = NativeModule.require('internal/process/esm_loader');
+    // Setup per-isolate callbacks that locate data or callbacks that we keep
+    // track of for different ESM modules.
+    setInitializeImportMetaObjectCallback(esm.initializeImportMetaObject);
+    setImportModuleDynamicallyCallback(esm.importModuleDynamicallyCallback);
+    const userLoader = getOptionValue('--loader');
+    // If --loader is specified, create a loader with user hooks. Otherwise
+    // create the default loader.
+    esm.initializeLoader(process.cwd(), userLoader);
+  }
+
   // For user code, we preload modules if `-r` is passed
   const preloadModules = getOptionValue('--require');
   if (preloadModules) {
diff --git a/lib/internal/process/esm_loader.js b/lib/internal/process/esm_loader.js
index f81053a1c3c3ad..0b7f1be6ff0595 100644
--- a/lib/internal/process/esm_loader.js
+++ b/lib/internal/process/esm_loader.js
@@ -1,8 +1,6 @@
 'use strict';
 
 const {
-  setImportModuleDynamicallyCallback,
-  setInitializeImportMetaObjectCallback,
   callbackMap,
 } = internalBinding('module_wrap');
 
@@ -15,16 +13,16 @@ const {
   ERR_VM_DYNAMIC_IMPORT_CALLBACK_MISSING,
 } = require('internal/errors').codes;
 
-function initializeImportMetaObject(wrap, meta) {
+exports.initializeImportMetaObject = function(wrap, meta) {
   if (callbackMap.has(wrap)) {
     const { initializeImportMeta } = callbackMap.get(wrap);
     if (initializeImportMeta !== undefined) {
       initializeImportMeta(meta, wrapToModuleMap.get(wrap) || wrap);
     }
   }
-}
+};
 
-async function importModuleDynamicallyCallback(wrap, specifier) {
+exports.importModuleDynamicallyCallback = async function(wrap, specifier) {
   if (callbackMap.has(wrap)) {
     const { importModuleDynamically } = callbackMap.get(wrap);
     if (importModuleDynamically !== undefined) {
@@ -33,10 +31,7 @@ async function importModuleDynamicallyCallback(wrap, specifier) {
     }
   }
   throw new ERR_VM_DYNAMIC_IMPORT_CALLBACK_MISSING();
-}
-
-setInitializeImportMetaObjectCallback(initializeImportMetaObject);
-setImportModuleDynamicallyCallback(importModuleDynamicallyCallback);
+};
 
 let loaderResolve;
 exports.loaderPromise = new Promise((resolve, reject) => {
@@ -45,13 +40,12 @@ exports.loaderPromise = new Promise((resolve, reject) => {
 
 exports.ESMLoader = undefined;
 
-exports.setup = function() {
+exports.initializeLoader = function(cwd, userLoader) {
   let ESMLoader = new Loader();
   const loaderPromise = (async () => {
-    const userLoader = require('internal/options').getOptionValue('--loader');
     if (userLoader) {
       const hooks = await ESMLoader.import(
-        userLoader, pathToFileURL(`${process.cwd()}/`).href);
+        userLoader, pathToFileURL(`${cwd}/`).href);
       ESMLoader = new Loader();
       ESMLoader.hook(hooks);
       exports.ESMLoader = ESMLoader;