diff --git a/spec/app/window-spec.coffee b/spec/app/window-spec.coffee
index 63fe2b58b..270ab8f96 100644
--- a/spec/app/window-spec.coffee
+++ b/spec/app/window-spec.coffee
@@ -3,7 +3,6 @@ fs = require 'fs'
 
 describe "Window", ->
   beforeEach ->
-    spyOn(window, 'loadUserConfiguration')
     window.startup()
 
   afterEach ->
diff --git a/spec/spec-helper.coffee b/spec/spec-helper.coffee
index 6415aceba..c8dc5d733 100644
--- a/spec/spec-helper.coffee
+++ b/spec/spec-helper.coffee
@@ -4,6 +4,7 @@ _ = require 'underscore'
 Keymap = require 'keymap'
 Point = require 'point'
 Directory = require 'directory'
+RootView = require 'root-view'
 require 'window'
 window.showConsole()
 
@@ -17,6 +18,7 @@ beforeEach ->
   directoriesWithSubscriptions = []
 
 afterEach ->
+  delete window.rootView if window.rootView
   $('#jasmine-content').empty()
   document.title = defaultTitle
   ensureNoDirectorySubscriptions()
@@ -24,6 +26,9 @@ afterEach ->
 window.keymap.bindKeys '*', 'meta-w': 'close'
 $(document).on 'close', -> window.close()
 
+# Don't load user configuration in specs, because it's variable
+RootView.prototype.loadUserConfiguration = ->
+
 Directory.prototype.originalOn = Directory.prototype.on
 Directory.prototype.on = (args...) ->
   directoriesWithSubscriptions.push(this) if @subscriptionCount() == 0
diff --git a/src/app/root-view.coffee b/src/app/root-view.coffee
index b04ae057d..eadf7bc7a 100644
--- a/src/app/root-view.coffee
+++ b/src/app/root-view.coffee
@@ -21,23 +21,24 @@ class RootView extends View
         @div id: 'panes', outlet: 'panes'
 
   @deserialize: ({ projectPath, panesViewState, extensionStates }) ->
-    rootView = new RootView(projectPath)
+    rootView = new RootView(projectPath, extensionStates: extensionStates, suppressOpen: true)
     rootView.setRootPane(rootView.deserializeView(panesViewState)) if panesViewState
-    rootView.extensionStates = extensionStates if extensionStates
     rootView
 
   extensions: null
   extensionStates: null
   fontSize: 20
 
-  initialize: (pathToOpen) ->
-    @extensions = {}
-    @extensionStates = {}
-    @project = new Project(pathToOpen)
+  initialize: (pathToOpen, { @extensionStates, suppressOpen } = {}) ->
+    window.rootView = this
 
+    @extensionStates ?= {}
+    @extensions = {}
+    @project = new Project(pathToOpen)
     @handleEvents()
     @setTitle()
-    @open(pathToOpen) if fs.isFile(pathToOpen)
+    @loadUserConfiguration()
+    @open(pathToOpen) if fs.isFile(pathToOpen) unless suppressOpen
 
   serialize: ->
     projectPath: @project?.getPath()
@@ -170,3 +171,11 @@ class RootView extends View
     @trigger 'font-size-change' if oldFontSize != newFontSize
 
   getFontSize: -> @fontSize
+
+  loadUserConfiguration: ->
+    try
+      require atom.userConfigurationPath if fs.exists(atom.userConfigurationPath)
+    catch error
+      console.error "Failed to load `#{atom.userConfigurationPath}`", error.message, error
+      window.showConsole()
+
diff --git a/src/app/window.coffee b/src/app/window.coffee
index 05b7854d6..97031bf8a 100644
--- a/src/app/window.coffee
+++ b/src/app/window.coffee
@@ -5,6 +5,7 @@ Native = require 'native'
 fs = require 'fs'
 _ = require 'underscore'
 $ = require 'jquery'
+{CoffeeScript} = require 'coffee-script'
 
 windowAdditions =
   rootViewParentSelector: 'body'
@@ -23,7 +24,6 @@ windowAdditions =
 
   startup: (path) ->
     @attachRootView(path)
-    @loadUserConfiguration()
     $(window).on 'close', => @close()
     $(window).on 'beforeunload', =>
       @shutdown()
@@ -38,23 +38,17 @@ windowAdditions =
     $(window).off('before')
     atom.windowClosed this
 
+  # Note: RootView assigns itself on window on initialization so that
+  # window.rootView is available when loading user configuration
   attachRootView: (pathToOpen) ->
-    rootViewState = atom.rootViewStates[$windowNumber]
-    if rootViewState
-      @rootView = RootView.deserialize(JSON.parse(rootViewState))
+    if rootViewState = atom.rootViewStates[$windowNumber]
+      RootView.deserialize(JSON.parse(rootViewState))
     else
-      @rootView = new RootView(pathToOpen)
+      new RootView(pathToOpen)
       @rootView.open() unless pathToOpen
 
     $(@rootViewParentSelector).append @rootView
 
-  loadUserConfiguration: ->
-    try
-      require atom.userConfigurationPath if fs.exists(atom.userConfigurationPath)
-    catch error
-      console.error "Failed to load `#{atom.userConfigurationPath}`", error.message, error
-      @showConsole()
-
   requireStylesheet: (path) ->
     fullPath = require.resolve(path)
     content = fs.read(fullPath)