diff --git a/__tests__/commands/run.js b/__tests__/commands/run.js
index 1912e76413..ba691cc1eb 100644
--- a/__tests__/commands/run.js
+++ b/__tests__/commands/run.js
@@ -71,8 +71,7 @@ test('lists all available commands with no arguments', (): Promise<void> => {
   return runRun({}, [], 'no-args', (config, reporter): ?Promise<void> => {
     const rprtr = new reporters.BufferReporter({stdout: null, stdin: null});
     const scripts = ['build', 'prestart', 'start'];
-    // Notice `cat-names` is below twice as there is a bug with output duplication
-    const bins = ['cat-names', 'cat-names'];
+    const bins = ['cat-names'];
 
     // Emulate run output
     rprtr.error(rprtr.lang('commandNotSpecified'));
diff --git a/src/cli/commands/run.js b/src/cli/commands/run.js
index 56b7b215c1..53828c5b54 100644
--- a/src/cli/commands/run.js
+++ b/src/cli/commands/run.js
@@ -30,14 +30,18 @@ export async function run(
   const pkg = await config.readManifest(config.cwd);
   const scripts = map();
   const binCommands = [];
+  const visitedBinFolders = new Set();
   let pkgCommands = [];
   for (const registry of Object.keys(registries)) {
     const binFolder = path.join(config.cwd, config.registries[registry].folder, '.bin');
-    if (await fs.exists(binFolder)) {
-      for (const name of await fs.readdir(binFolder)) {
-        binCommands.push(name);
-        scripts[name] = `"${path.join(binFolder, name)}"`;
+    if (!visitedBinFolders.has(binFolder)) {
+      if (await fs.exists(binFolder)) {
+        for (const name of await fs.readdir(binFolder)) {
+          binCommands.push(name);
+          scripts[name] = `"${path.join(binFolder, name)}"`;
+        }
       }
+      visitedBinFolders.add(binFolder);
     }
   }
   if (pkg.scripts) {