diff --git a/src/browser/atom-application.coffee b/src/browser/atom-application.coffee
index 8e1f66ec0..402a3f3ed 100644
--- a/src/browser/atom-application.coffee
+++ b/src/browser/atom-application.coffee
@@ -70,7 +70,7 @@ class AtomApplication
 
     @autoUpdateManager = new AutoUpdateManager(@version)
     @applicationMenu = new ApplicationMenu(@version)
-    @atomProtocolHandler = new AtomProtocolHandler(@resourcePath)
+    @atomProtocolHandler = new AtomProtocolHandler(@resourcePath, @safeMode)
 
     @listenForArgumentsFromNewProcess()
     @setupJavaScriptArguments()
diff --git a/src/browser/atom-protocol-handler.coffee b/src/browser/atom-protocol-handler.coffee
index 6777a21ee..d6c1f567b 100644
--- a/src/browser/atom-protocol-handler.coffee
+++ b/src/browser/atom-protocol-handler.coffee
@@ -5,16 +5,26 @@ protocol = require 'protocol'
 
 # Handles requests with 'atom' protocol.
 #
-# It's created by {AtomApplication} upon instantiation, and is used to create a
-# custom resource loader by adding the 'atom' custom protocol.
+# It's created by {AtomApplication} upon instantiation and is used to create a
+# custom resource loader for 'atom://' URLs.
+#
+# The following directories are searched in order:
+#   * ~/.atom/assets
+#   * ~/.atom/dev/packages (unless in safe mode)
+#   * ~/.atom/packages
+#   * RESOURCE_PATH/node_modules
+#
 module.exports =
 class AtomProtocolHandler
-  constructor: (@resourcePath) ->
-    @loadPaths = [
-      path.join(app.getHomeDir(), '.atom', 'dev', 'packages')
-      path.join(app.getHomeDir(), '.atom', 'packages')
-      path.join(@resourcePath, 'node_modules')
-    ]
+  constructor: (resourcePath, safeMode) ->
+    @loadPaths = []
+    @dotAtomDirectory = path.join(app.getHomeDir(), '.atom')
+
+    unless safeMode
+      @loadPaths.push(path.join(@dotAtomDirectory, 'dev', 'packages'))
+
+    @loadPaths.push(path.join(@dotAtomDirectory, 'packages'))
+    @loadPaths.push(path.join(resourcePath, 'node_modules'))
 
     @registerAtomProtocol()
 
@@ -22,7 +32,14 @@ class AtomProtocolHandler
   registerAtomProtocol: ->
     protocol.registerProtocol 'atom', (request) =>
       relativePath = path.normalize(request.url.substr(7))
-      for loadPath in @loadPaths
-        filePath = path.join(loadPath, relativePath)
-        break if fs.statSyncNoException(filePath).isFile?()
-      return new protocol.RequestFileJob(filePath)
+
+      if relativePath.indexOf('assets/') is 0
+        assetsPath = path.join(@dotAtomDirectory, relativePath)
+        filePath = assetsPath if fs.statSyncNoException(assetsPath).isFile?()
+
+      unless filePath
+        for loadPath in @loadPaths
+          filePath = path.join(loadPath, relativePath)
+          break if fs.statSyncNoException(filePath).isFile?()
+
+      new protocol.RequestFileJob(filePath)