diff --git a/src/config.js b/src/config.js
index 4accbef1aa..f48f92a2b4 100644
--- a/src/config.js
+++ b/src/config.js
@@ -177,7 +177,6 @@ export default class Config {
     await fs.mkdirp(this.globalFolder);
     await fs.mkdirp(this.cacheFolder);
     await fs.mkdirp(this.tempFolder);
-
     await fs.mkdirp(this.linkFolder);
 
     this.linkedModules = [];
@@ -185,9 +184,13 @@ export default class Config {
     const maybeLinkedModules = await fs.readdir(this.linkFolder);
 
     for (const maybeLinked of maybeLinkedModules) {
-      // handle scoped modules separately
-      if (maybeLinked.indexOf('@') === 0) {
-        const scopedLinked = await fs.readdir(path.join(this.linkFolder, maybeLinked));
+      const linkedPath = path.join(this.linkFolder, maybeLinked);
+      const isScopedName = maybeLinked.indexOf('@') === 0;
+      const isScopedContainer = isScopedName && !await fs.exists(path.join(linkedPath, 'package.json'));
+
+      // handle scoped containers (npm scoped modules) separately
+      if (isScopedContainer) {
+        const scopedLinked = await fs.readdir(linkedPath);
         this.linkedModules.push(...scopedLinked.map((dir) => path.join(maybeLinked, dir)));
       } else {
         this.linkedModules.push(maybeLinked);
diff --git a/src/package-linker.js b/src/package-linker.js
index 2c7a3d3120..d5accdd2ef 100644
--- a/src/package-linker.js
+++ b/src/package-linker.js
@@ -159,11 +159,14 @@ export default class PackageLinker {
         const files = await fs.readdir(loc);
         for (const file of files) {
           const filePath = path.join(loc, file);
-          // scoped packages are a nested one level deeper
-          if (file.indexOf('@') === 0) {
+
+          const isScopedName = file.indexOf('@') === 0;
+          const isScopedContainer = isScopedName && !await fs.exists(path.join(loc, 'package.json'));
+          // npm scoped packages are a nested one level deeper
+          if (isScopedContainer) {
             const scopedFiles = await fs.readdir(filePath);
-            for (const scoped of scopedFiles) {
-              possibleExtraneous.add(path.join(filePath, scoped));
+            for (const scopedFile of scopedFiles) {
+              possibleExtraneous.add(path.join(filePath, scopedFile));
             }
           } else {
             possibleExtraneous.add(filePath);