diff --git a/src/browser/atom-application.coffee b/src/browser/atom-application.coffee
index 1b2aa2e86..ae56fb1d4 100644
--- a/src/browser/atom-application.coffee
+++ b/src/browser/atom-application.coffee
@@ -99,12 +99,12 @@ class AtomApplication
 
   # Public: Removes the {AtomWindow} from the global window list.
   removeWindow: (window) ->
-    @windows.splice @windows.indexOf(window), 1
-    if @windows.length is 0
+    if @windows.length is 1
       @applicationMenu?.enableWindowSpecificItems(false)
       if process.platform in ['win32', 'linux']
         app.quit()
         return
+    @windows.splice(@windows.indexOf(window), 1)
     @saveState() unless window.isSpec or @quitting
 
   # Public: Adds the {AtomWindow} to the global window list.
@@ -210,6 +210,7 @@ class AtomApplication
     @openPathOnEvent('application:open-license', path.join(process.resourcesPath, 'LICENSE.md'))
 
     app.on 'before-quit', =>
+      @saveState() if @hasEditorWindows()
       @quitting = true
 
     app.on 'will-quit', =>
@@ -217,7 +218,7 @@ class AtomApplication
       @deleteSocketFile()
 
     app.on 'will-exit', =>
-      @saveState() unless @windows.every (window) -> window.isSpec
+      @saveState() if @hasEditorWindows()
       @killAllProcesses()
       @deleteSocketFile()
 
@@ -435,6 +436,9 @@ class AtomApplication
           states.push(initialPaths: loadSettings.initialPaths)
     @storageFolder.store('application.json', states)
 
+  hasEditorWindows: ->
+    @windows.some (window) -> not window.isSpec
+
   loadState: ->
     if (states = @storageFolder.load('application.json'))?.length > 0
       for state in states