diff --git a/packages/babel-register/package.json b/packages/babel-register/package.json
index 949f5498b8..8c4f92813d 100644
--- a/packages/babel-register/package.json
+++ b/packages/babel-register/package.json
@@ -14,7 +14,7 @@
   "author": "Sebastian McKenzie <sebmck@gmail.com>",
   "main": "lib/index.js",
   "browser": {
-    "./lib/node.js": "./lib/browser.js"
+    "./lib/nodeWrapper.js": "./lib/browser.js"
   },
   "dependencies": {
     "find-cache-dir": "^2.0.0",
diff --git a/packages/babel-register/src/index.js b/packages/babel-register/src/index.js
index baf93d9367..aea88df53e 100644
--- a/packages/babel-register/src/index.js
+++ b/packages/babel-register/src/index.js
@@ -9,7 +9,7 @@ exports = module.exports = function (...args) {
 };
 exports.__esModule = true;
 
-const node = require("./node");
+const node = require("./nodeWrapper");
 const register = node.default;
 
 Object.assign(exports, node);
diff --git a/packages/babel-register/src/node.js b/packages/babel-register/src/node.js
index ed527cdac5..a27b0c87fd 100644
--- a/packages/babel-register/src/node.js
+++ b/packages/babel-register/src/node.js
@@ -7,6 +7,7 @@ import { OptionManager, DEFAULT_EXTENSIONS } from "@babel/core";
 import { addHook } from "pirates";
 import fs from "fs";
 import path from "path";
+import Module from "module";
 
 const maps = {};
 let transformOpts = {};
@@ -82,15 +83,19 @@ function compile(code, filename) {
 }
 
 let compiling = false;
+const internalModuleCache = Module._cache;
 
 function compileHook(code, filename) {
   if (compiling) return code;
 
+  const globalModuleCache = Module._cache;
   try {
     compiling = true;
+    Module._cache = internalModuleCache;
     return compile(code, filename);
   } finally {
     compiling = false;
+    Module._cache = globalModuleCache;
   }
 }
 
diff --git a/packages/babel-register/src/nodeWrapper.js b/packages/babel-register/src/nodeWrapper.js
new file mode 100644
index 0000000000..97666b3ef9
--- /dev/null
+++ b/packages/babel-register/src/nodeWrapper.js
@@ -0,0 +1,21 @@
+/**
+ * This file wraps the implementation of register so all modules `require()`-ed
+ * internally within register are stored in a separate module cache.
+ * This prevents un-transformed modules being stored in global module cache,
+ * and allows register to transform these modules if they are loaded externally.
+ */
+
+const Module = require("module");
+
+const globalModuleCache = Module._cache;
+const internalModuleCache = Object.create(null);
+
+Module._cache = internalModuleCache;
+const node = require("./node");
+Module._cache = globalModuleCache;
+
+// Add source-map-support to global cache as it's stateful
+const smsPath = require.resolve("source-map-support");
+globalModuleCache[smsPath] = internalModuleCache[smsPath];
+
+module.exports = node;
diff --git a/packages/babel-register/test/fixtures/internal-modules/index.js b/packages/babel-register/test/fixtures/internal-modules/index.js
new file mode 100644
index 0000000000..d59a323368
--- /dev/null
+++ b/packages/babel-register/test/fixtures/internal-modules/index.js
@@ -0,0 +1,28 @@
+const register = require('../../..');
+
+// Plugin to add '/* transformed */' comment to start of function bodies
+const plugin = () => ( {
+  visitor: {
+    Function(path) {
+      const bodyNode = path.node.body;
+      (bodyNode.leadingComments || (bodyNode.leadingComments = [])).push( {
+        type: 'CommentBlock',
+        value: ' transformed '
+      } );
+    },
+  },
+} );
+
+register( {
+  ignore: [],
+  babelrc: false,
+  configFile: false,
+  plugins: [plugin]
+} );
+
+console.log(
+  JSON.stringify({
+    convertSourceMap: require('convert-source-map').fromObject.toString(),
+    isPlainObject: require('lodash/isPlainObject').toString()
+  })
+);
diff --git a/packages/babel-register/test/index.js b/packages/babel-register/test/index.js
index ca594af663..181a768bb8 100644
--- a/packages/babel-register/test/index.js
+++ b/packages/babel-register/test/index.js
@@ -6,7 +6,7 @@ let currentHook;
 let currentOptions;
 let sourceMapSupport = false;
 
-const registerFile = require.resolve("../lib/node");
+const registerFile = require.resolve("../lib/index");
 const testCacheFilename = path.join(__dirname, ".babel");
 const testFile = require.resolve("./fixtures/babelrc/es2015");
 const testFileContent = fs.readFileSync(testFile);
@@ -14,6 +14,9 @@ const sourceMapTestFile = require.resolve("./fixtures/source-map/index");
 const sourceMapNestedTestFile = require.resolve(
   "./fixtures/source-map/foo/bar",
 );
+const internalModulesTestFile = require.resolve(
+  "./fixtures/internal-modules/index",
+);
 
 jest.mock("pirates", () => {
   return {
@@ -152,18 +155,7 @@ describe("@babel/register", function () {
     // that working inside a test, possibly because of jest’s mocking
     // hooks, so we spawn a separate process.
 
-    const args = ["-r", registerFile, sourceMapTestFile];
-    const spawn = child.spawn(process.execPath, args, { cwd: __dirname });
-
-    let output = "";
-
-    for (const stream of [spawn.stderr, spawn.stdout]) {
-      stream.on("data", chunk => {
-        output += chunk;
-      });
-    }
-
-    spawn.on("close", function () {
+    spawnNode(["-r", registerFile, sourceMapTestFile], output => {
       let err;
 
       try {
@@ -201,4 +193,40 @@ describe("@babel/register", function () {
 
     expect(result).toBe('"use strict";\n\nrequire("assert");');
   });
+
+  test("transforms modules used within register", callback => {
+    // Need a clean environment without `convert-source-map`
+    // and `lodash/isPlainObject` already in the require cache,
+    // so we spawn a separate process
+
+    spawnNode([internalModulesTestFile], output => {
+      let err;
+
+      try {
+        const { convertSourceMap, isPlainObject } = JSON.parse(output);
+        expect(convertSourceMap).toMatch("/* transformed */");
+        expect(isPlainObject).toMatch("/* transformed */");
+      } catch (e) {
+        err = e;
+      }
+
+      callback(err);
+    });
+  });
 });
+
+function spawnNode(args, callback) {
+  const spawn = child.spawn(process.execPath, args, { cwd: __dirname });
+
+  let output = "";
+
+  for (const stream of [spawn.stderr, spawn.stdout]) {
+    stream.on("data", chunk => {
+      output += chunk;
+    });
+  }
+
+  spawn.on("close", function () {
+    callback(output);
+  });
+}