diff --git a/src/babel/transformation/file/plugin-manager.js b/src/babel/transformation/file/plugin-manager.js
index 21258797ac..b82a3c29cf 100644
--- a/src/babel/transformation/file/plugin-manager.js
+++ b/src/babel/transformation/file/plugin-manager.js
@@ -57,6 +57,9 @@ export default class PluginManager {
     if (!plugin.buildPass || plugin.constructor.name !== "Transformer") {
       throw new TypeError(messages.get("pluginNotTransformer", name));
     }
+
+    // register as a plugin
+    plugin.metadata.plugin = true;
   }
 
   add(name) {
diff --git a/src/babel/transformation/transformer-pipeline.js b/src/babel/transformation/transformer-pipeline.js
index 7d6afc0a4a..5a4c704b49 100644
--- a/src/babel/transformation/transformer-pipeline.js
+++ b/src/babel/transformation/transformer-pipeline.js
@@ -47,6 +47,8 @@ export default class TransformerPipeline {
   }
 
   canTransform(transformer, fileOpts) {
+    if (transformer.metadata.plugin) return true;
+
     for (var filter of (this.filters: Array)) {
       var result = filter(transformer, fileOpts);
       if (result != null) return result;