diff --git a/src/pyodide/BUILD.bazel b/src/pyodide/BUILD.bazel
index ea1c76548d9..aa0695d5526 100644
--- a/src/pyodide/BUILD.bazel
+++ b/src/pyodide/BUILD.bazel
@@ -178,14 +178,19 @@ esbuild(
     config = "internal/pool/esbuild.config.mjs",
     entry_point = "internal/pool/emscriptenSetup.ts",
     external = [
+        "child_process",
+        "crypto",
         "fs",
         "path",
         "url",
         "vm",
-        "path",
-        "crypto",
         "ws",
-        "child_process",
+        "node:child_process",
+        "node:crypto",
+        "node:fs",
+        "node:path",
+        "node:url",
+        "node:vm",
     ],
     format = "esm",
     output = "generated/emscriptenSetup.js",
diff --git a/src/pyodide/internal/pool/builtin_wrappers.ts b/src/pyodide/internal/pool/builtin_wrappers.ts
index dbb31d27518..4ddefd635fd 100644
--- a/src/pyodide/internal/pool/builtin_wrappers.ts
+++ b/src/pyodide/internal/pool/builtin_wrappers.ts
@@ -68,11 +68,35 @@ export function monotonicDateNow(): number {
  *      - ctypes is quite slow even by Python's standards
  *      - Normally ctypes allocates all closures up front
  */
+let finishedSetup = false;
+export function finishSetup() {
+  finishedSetup = true;
+}
+
 export function newWasmModule(buffer: Uint8Array): WebAssembly.Module {
-  checkCallee();
+  if (finishedSetup) {
+    checkCallee();
+  }
   return UnsafeEval.newWasmModule(buffer);
 }
 
+export async function wasmInstantiate(
+  mod: WebAssembly.Module | Uint8Array,
+  imports: WebAssembly.Imports
+): Promise<{ module: WebAssembly.Module; instance: WebAssembly.Instance }> {
+  let module;
+  if (mod instanceof WebAssembly.Module) {
+    module = mod;
+  } else {
+    if (finishedSetup) {
+      checkCallee();
+    }
+    module = UnsafeEval.newWasmModule(mod);
+  }
+  const instance = new WebAssembly.Instance(module, imports);
+  return { module, instance };
+}
+
 /**
  * Check that the callee is `convertJsFunctionToWasm` by formatting a stack
  * trace and using `prepareStackTrace` to read out the callee. It should be
@@ -120,18 +144,3 @@ function prepareStackTrace(_error: Error, stack: StackItem[]): boolean {
     return false;
   }
 }
-
-export async function wasmInstantiate(
-  mod: WebAssembly.Module | Uint8Array,
-  imports: WebAssembly.Imports
-): Promise<{ module: WebAssembly.Module; instance: WebAssembly.Instance }> {
-  let module;
-  if (mod instanceof WebAssembly.Module) {
-    module = mod;
-  } else {
-    checkCallee();
-    module = UnsafeEval.newWasmModule(mod);
-  }
-  const instance = new WebAssembly.Instance(module, imports);
-  return { module, instance };
-}
diff --git a/src/pyodide/internal/pool/emscriptenSetup.ts b/src/pyodide/internal/pool/emscriptenSetup.ts
index d72946898c6..276c3c6be6a 100644
--- a/src/pyodide/internal/pool/emscriptenSetup.ts
+++ b/src/pyodide/internal/pool/emscriptenSetup.ts
@@ -16,6 +16,7 @@ import { _createPyodideModule } from 'pyodide-internal:generated/pyodide.asm';
 import {
   setUnsafeEval,
   setGetRandomValues,
+  finishSetup,
 } from 'pyodide-internal:pool/builtin_wrappers';
 
 /**
@@ -168,7 +169,7 @@ function getEmscriptenSettings(
 function* featureDetectionMonkeyPatchesContextManager() {
   const global = globalThis as any;
   // Make Emscripten think we're in the browser main thread
-  global.window = {};
+  global.window = { sessionStorage: {} };
   global.document = { createElement() {} };
   global.sessionStorage = {};
   // Make Emscripten think we're not in a worker
@@ -212,6 +213,7 @@ export async function instantiateEmscriptenModule(
     const emscriptenModule = await emscriptenSettings.readyPromise;
     emscriptenModule.setUnsafeEval = setUnsafeEval;
     emscriptenModule.setGetRandomValues = setGetRandomValues;
+    finishSetup();
     return emscriptenModule;
   } catch (e) {
     console.warn('Error in instantiateEmscriptenModule');