diff --git a/src/app/atom.coffee b/src/app/atom.coffee
index 0788f4b1d..c180f8d55 100644
--- a/src/app/atom.coffee
+++ b/src/app/atom.coffee
@@ -179,3 +179,10 @@ _.extend atom,
 
   getUpdateStatus: (callback) ->
     @sendMessageToBrowserProcess('getUpdateStatus', [], callback)
+
+  requireUserInitScript: ->
+    userInitScriptPath = fs.join(config.configDirPath, "user.coffee")
+    try
+      require userInitScriptPath if fs.isFile(userInitScriptPath)
+    catch error
+      console.error "Failed to load `#{userInitScriptPath}`", error.stack, error
diff --git a/src/app/config.coffee b/src/app/config.coffee
index 00af004e0..2940b33f4 100644
--- a/src/app/config.coffee
+++ b/src/app/config.coffee
@@ -3,7 +3,6 @@ _ = require 'underscore'
 EventEmitter = require 'event-emitter'
 
 configDirPath = fs.absolute("~/.atom")
-userInitScriptPath = fs.join(configDirPath, "user.coffee")
 bundledPackagesDirPath = fs.join(resourcePath, "src/packages")
 bundledThemesDirPath = fs.join(resourcePath, "themes")
 vendoredPackagesDirPath = fs.join(resourcePath, "vendor/packages")
@@ -53,7 +52,6 @@ class Config
   load: ->
     @initializeConfigDirectory()
     @loadUserConfig()
-    @requireUserInitScript()
 
   loadUserConfig: ->
     if fs.exists(@configFilePath)
@@ -100,10 +98,4 @@ class Config
   save: ->
     fs.writeObject(@configFilePath, @settings)
 
-  requireUserInitScript: ->
-    try
-      require userInitScriptPath if fs.exists(userInitScriptPath)
-    catch error
-      console.error "Failed to load `#{userInitScriptPath}`", error.stack, error
-
 _.extend Config.prototype, EventEmitter
diff --git a/src/app/window.coffee b/src/app/window.coffee
index b401bcb66..63acc542a 100644
--- a/src/app/window.coffee
+++ b/src/app/window.coffee
@@ -49,6 +49,7 @@ window.startup = ->
   atom.loadThemes()
   atom.loadPackages()
   keymap.loadUserKeymaps()
+  atom.requireUserInitScript()
   $(window).on 'beforeunload', -> shutdown(); false
   $(window).focus()