diff --git a/build/Gruntfile.coffee b/build/Gruntfile.coffee
index e07f7363a..62672b1e4 100644
--- a/build/Gruntfile.coffee
+++ b/build/Gruntfile.coffee
@@ -40,7 +40,10 @@ module.exports = (grunt) ->
   appName = if process.platform is 'darwin' then 'Atom.app' else 'Atom'
   buildDir = grunt.option('build-dir') ? path.join(tmpDir, 'atom-build')
   installDir = grunt.option('install-dir')
-  atomShellDownloadDir = path.join(tmpDir, 'atom-cached-atom-shells')
+
+  home = if process.env is 'win32' then process.env.USERPROFILE else process.env.HOME
+  atomShellDownloadDir = path.join(home, '.atom', 'atom-shell')
+
   symbolsDir = path.join(buildDir, 'Atom.breakpad.syms')
   shellAppDir = path.join(buildDir, appName)
   if process.platform is 'win32'
diff --git a/script/clean b/script/clean
index 51e0f0590..236e9f58f 100755
--- a/script/clean
+++ b/script/clean
@@ -24,6 +24,7 @@ var commands = [
   [home, '.atom', 'storage'],
   [home, '.atom', '.npm'],
   [home, '.atom', 'compile-cache'],
+  [home, '.atom', 'atom-shell'],
   [tmpdir, 'atom-build'],
   [tmpdir, 'atom-cached-atom-shells'],
 ];