diff --git a/script/bootstrap b/script/bootstrap
index 609a7305c..ec14cfa49 100755
--- a/script/bootstrap
+++ b/script/bootstrap
@@ -24,6 +24,7 @@ var commands = [
   joinCommands('cd vendor/apm', 'npm install --silent .'),
   'npm install --silent vendor/apm',
   echoNewLine,
+  'node node_modules/atom-package-manager/bin/apm clean',
   'node node_modules/atom-package-manager/bin/apm install --silent',
 ];
 
diff --git a/script/cibuild b/script/cibuild
index 8ca3bf46a..c83d01c45 100755
--- a/script/cibuild
+++ b/script/cibuild
@@ -32,7 +32,6 @@ cp.safeExec.bind(global, 'node script/bootstrap', function(error) {
   async.series([
     require('rimraf').bind(global, path.join(homeDir, '.atom')),
     cp.safeExec.bind(global, 'git clean -dff'),
-    cp.safeExec.bind(global, 'node node_modules/atom-package-manager/bin/apm clean --no-color'),
     cp.safeExec.bind(global, 'node node_modules/grunt-cli/bin/grunt ci --stack --no-color'),
   ], function(error) {
     process.exit(error ? 1 : 0);