diff --git a/build-system/compile/compile.js b/build-system/compile/compile.js
index 76c55a4ec612..b036ebd9e24a 100644
--- a/build-system/compile/compile.js
+++ b/build-system/compile/compile.js
@@ -238,7 +238,7 @@ function compile(entryModuleFilenames, outputDir, outputFilename, options) {
       'node_modules/web-animations-js/web-animations.install.js',
       'node_modules/web-activities/activity-ports.js',
       'node_modules/@ampproject/animations/dist/animations.mjs',
-      'node_modules/@ampproject/worker-dom/dist/amp.main.mjs',
+      'node_modules/@ampproject/worker-dom/dist/amp/main.mjs',
       'node_modules/document-register-element/build/' +
         'document-register-element.patched.js',
       // 'node_modules/core-js/modules/**.js',
diff --git a/build-system/tasks/dep-check.js b/build-system/tasks/dep-check.js
index 921eabc5e894..8e055901ab89 100644
--- a/build-system/tasks/dep-check.js
+++ b/build-system/tasks/dep-check.js
@@ -29,6 +29,7 @@ const source = require('vinyl-source-stream');
 const through = require('through2');
 const {createCtrlcHandler, exitCtrlcHandler} = require('../ctrlcHandler');
 const {css} = require('./css');
+const {devDependencies} = require('./helpers');
 const {isTravisBuild} = require('../travis');
 
 const root = process.cwd();
@@ -207,9 +208,9 @@ function getGraph(entryModule) {
   // we're not running browserify twice on travis.
   const bundler = browserify(entryModule, {debug: true}).transform(babelify, {
     compact: false,
-    // Transform files in node_modules since deps use ES6 export.
-    // https://github.com/babel/babelify#why-arent-files-in-node_modules-being-transformed
+    // Transform "node_modules/", but ignore devDependencies.
     global: true,
+    ignore: devDependencies(),
   });
 
   bundler.pipeline.get('deps').push(
diff --git a/build-system/tasks/helpers.js b/build-system/tasks/helpers.js
index d7f6b5b6a17d..521b65deb416 100644
--- a/build-system/tasks/helpers.js
+++ b/build-system/tasks/helpers.js
@@ -404,6 +404,17 @@ function finishBundle(srcFilename, destDir, destFilename, options) {
   }
 }
 
+/**
+ * Returns array of relative paths to "devDependencies" defined in package.json.
+ * @return {!Array<string>}
+ */
+function devDependencies() {
+  const file = fs.readFileSync('package.json', 'utf8');
+  const packageJson = JSON.parse(file);
+  const devDependencies = Object.keys(packageJson['devDependencies']);
+  return devDependencies.map(p => `./node_modules/${p}`);
+}
+
 /**
  * Transforms a given JavaScript file entry point with browserify, and watches
  * it for changes (if required).
@@ -422,7 +433,11 @@ function compileUnminifiedJs(srcDir, srcFilename, destDir, options) {
   let bundler = browserify({
     entries: entryPoint,
     debug: true,
-  }).transform(babelify);
+  }).transform(babelify, {
+    // Transform "node_modules/", but ignore devDependencies.
+    global: true,
+    ignore: devDependencies(),
+  });
 
   if (options.watch) {
     bundler = watchify(bundler);
@@ -751,6 +766,7 @@ module.exports = {
   compileAllUnminifiedTargets,
   compileJs,
   compileTs,
+  devDependencies,
   enableLocalTesting,
   endBuildStep,
   hostname,
diff --git a/build-system/tasks/karma.conf.js b/build-system/tasks/karma.conf.js
index 14d51f5a0488..e82611fbc3b1 100644
--- a/build-system/tasks/karma.conf.js
+++ b/build-system/tasks/karma.conf.js
@@ -15,6 +15,7 @@
  */
 'use strict';
 
+const {devDependencies} = require('./helpers');
 const {gitCommitterEmail} = require('../git');
 const {isTravisBuild, travisJobNumber} = require('../travis');
 
@@ -68,7 +69,15 @@ module.exports = {
     debug: true,
     basedir: __dirname + '/../../',
     transform: [
-      ['babelify', {'global': isTravisBuild(), 'sourceMapsAbsolute': true}],
+      [
+        'babelify',
+        {
+          // Transform "node_modules/", but ignore devDependencies (on Travis).
+          'global': isTravisBuild(),
+          'ignore': devDependencies(),
+          'sourceMapsAbsolute': true,
+        },
+      ],
     ],
     // Prevent "cannot find module" errors on Travis. See #14166.
     bundleDelay: isTravisBuild() ? 5000 : 1200,
diff --git a/build-system/tasks/update-packages.js b/build-system/tasks/update-packages.js
index 3b6a9bc13f0a..9e8525130e8b 100644
--- a/build-system/tasks/update-packages.js
+++ b/build-system/tasks/update-packages.js
@@ -118,46 +118,6 @@ function patchRegisterElement() {
   );
 }
 
-/**
- * transformEs6Packages() doesn't work on subdirectories of dist/,
- * and I can't figure out which option enables it.
- * Just move "dist/amp/main.mjs" to "dist/amp.main.mjs" as a workaround.
- */
-function moveWorkerDom() {
-  const dir = 'node_modules/@ampproject/worker-dom/dist/';
-  fs.copyFileSync(dir + 'amp/main.mjs', dir + 'amp.main.mjs');
-}
-
-/**
- * Makes sure ES6 packages in node_modules that are used by the runtime will be
- * transformed by babelify. The list of packages is dynamically generated by
- * reading the `dependencies` section of the package.json in the project root.
- * This is a no-op if transforms are already enabled for a package.
- * See https://github.com/babel/babelify#why-arent-files-in-node_modules-being-transformed
- */
-function transformEs6Packages() {
-  const rootPackageJsonFile = 'package.json';
-  const rootPackageJsonContents = fs.readFileSync(rootPackageJsonFile, 'utf8');
-  const rootPackageJson = JSON.parse(rootPackageJsonContents);
-  const es6Packages = Object.keys(rootPackageJson['dependencies']);
-  es6Packages.forEach(es6Package => {
-    const packageJsonFile = 'node_modules/' + es6Package + '/package.json';
-    const packageJsonContents = fs.readFileSync(packageJsonFile, 'utf8');
-    const packageJson = JSON.parse(packageJsonContents);
-    if (!packageJson['browserify']) {
-      packageJson['browserify'] = {'transform': ['babelify']};
-      const updatedPackageJson = JSON.stringify(packageJson, null, 2);
-      fs.writeFileSync(packageJsonFile, updatedPackageJson, 'utf8');
-      if (!isTravisBuild()) {
-        log(
-          colors.green('Enabled ES6 transforms for runtime dependency'),
-          colors.cyan(es6Package)
-        );
-      }
-    }
-  });
-}
-
 /**
  * Installs custom lint rules from build-system/eslint-rules to node_modules.
  */
@@ -226,8 +186,6 @@ async function updatePackages() {
   }
   patchWebAnimations();
   patchRegisterElement();
-  moveWorkerDom();
-  transformEs6Packages();
 }
 
 module.exports = {
diff --git a/extensions/amp-script/0.1/amp-script.js b/extensions/amp-script/0.1/amp-script.js
index 4fa3e891d3ca..5bbad89c258c 100644
--- a/extensions/amp-script/0.1/amp-script.js
+++ b/extensions/amp-script/0.1/amp-script.js
@@ -35,7 +35,7 @@ import {
 } from '../../../src/service/origin-experiments-impl';
 import {isExperimentOn} from '../../../src/experiments';
 import {rewriteAttributeValue} from '../../../src/url-rewrite';
-import {upgrade} from '@ampproject/worker-dom/dist/amp.main.mjs';
+import {upgrade} from '@ampproject/worker-dom/dist/amp/main.mjs';
 
 /** @const {string} */
 const TAG = 'amp-script';