diff --git a/packages/babel-core/src/transformation/file/options/option-manager.js b/packages/babel-core/src/transformation/file/options/option-manager.js
index 9ed73aa717..f8a787783f 100644
--- a/packages/babel-core/src/transformation/file/options/option-manager.js
+++ b/packages/babel-core/src/transformation/file/options/option-manager.js
@@ -401,6 +401,11 @@ export default class OptionManager {
   init(opts: Object = {}): Object {
     let filename = opts.filename;
 
+    // resolve all .babelrc files
+    if (opts.babelrc !== false) {
+      this.findConfigs(filename);
+    }
+
     // merge in base options
     this.mergeOptions({
       options: opts,
@@ -408,11 +413,6 @@ export default class OptionManager {
       dirname: filename && path.dirname(filename)
     });
 
-    // resolve all .babelrc files
-    if (this.options.babelrc !== false) {
-      this.findConfigs(filename);
-    }
-
     // normalise
     this.normaliseOptions(opts);
 
diff --git a/packages/babel-register/src/node.js b/packages/babel-register/src/node.js
index 1c72e48f80..da9a08e87c 100644
--- a/packages/babel-register/src/node.js
+++ b/packages/babel-register/src/node.js
@@ -49,16 +49,10 @@ function mtime(filename) {
 function compile(filename) {
   let result;
 
-  let optsManager = new OptionManager;
-
   // merge in base options and resolve all the plugins and presets relative to this file
-  optsManager.mergeOptions({
-    options: deepClone(transformOpts),
-    alias: "base",
-    dirname: path.dirname(filename)
-  });
-
-  let opts = optsManager.init({ filename });
+  let opts = new OptionManager().init(extend(deepClone(transformOpts), {
+    filename
+  }));
 
   let cacheKey = `${JSON.stringify(opts)}:${babel.version}`;