diff --git a/packages/babel-core/src/config/option-manager.js b/packages/babel-core/src/config/option-manager.js
index 9f65f4762d..4d8cac0395 100644
--- a/packages/babel-core/src/config/option-manager.js
+++ b/packages/babel-core/src/config/option-manager.js
@@ -120,6 +120,7 @@ class OptionManager {
 
     // Tack the passes onto the object itself so that, if this object is passed back to Babel a second time,
     // it will be in the right structure to not change behavior.
+    opts.babelrc = false;
     opts.plugins = this.passes[0];
     opts.presets = this.passes
       .slice(1)
diff --git a/packages/babel-register/src/node.js b/packages/babel-register/src/node.js
index f4715ff35d..21729f4fdb 100644
--- a/packages/babel-register/src/node.js
+++ b/packages/babel-register/src/node.js
@@ -63,16 +63,11 @@ function compile(code, filename) {
     }
   }
 
-  const result = babel.transform(
-    code,
-    Object.assign(opts, {
-      // Do not process config files since has already been done with the OptionManager
-      // calls above and would introduce duplicates.
-      babelrc: false,
-      sourceMaps: opts.sourceMaps === undefined ? "both" : opts.sourceMaps,
-      ast: false,
-    }),
-  );
+  const result = babel.transform(code, {
+    ...opts,
+    sourceMaps: opts.sourceMaps === undefined ? "both" : opts.sourceMaps,
+    ast: false,
+  });
 
   if (cache) {
     cache[cacheKey] = result;