diff --git a/src/atom.coffee b/src/atom.coffee
index 0d029b61d..2639eaca6 100644
--- a/src/atom.coffee
+++ b/src/atom.coffee
@@ -763,7 +763,8 @@ class Atom extends Model
   # Notify the browser project of the window's current project path
   watchProjectPath: ->
     @disposables.add @project.onDidChangePaths =>
-      @constructor.updateLoadSetting('initialPaths', @project.getPaths())
+      @constructor.updateLoadSetting('initialPaths',
+        @project.getPaths().filter((projectPath) -> fs.existsSync(projectPath)))
 
   exit: (status) ->
     app = remote.require('app')