diff --git a/atom/browser/api/atom_api_download_item.cc b/atom/browser/api/atom_api_download_item.cc
index ec4dcd84b285..691cfbfef594 100644
--- a/atom/browser/api/atom_api_download_item.cc
+++ b/atom/browser/api/atom_api_download_item.cc
@@ -6,6 +6,7 @@
 
 #include <map>
 
+#include "atom/browser/atom_browser_main_parts.h"
 #include "atom/common/native_mate_converters/callback.h"
 #include "atom/common/native_mate_converters/file_path_converter.h"
 #include "atom/common/native_mate_converters/gurl_converter.h"
@@ -159,14 +160,6 @@ mate::ObjectTemplateBuilder DownloadItem::GetObjectTemplateBuilder(
       .SetMethod("setSavePath", &DownloadItem::SetSavePath);
 }
 
-void SetWrapDownloadItem(const WrapDownloadItemCallback& callback) {
-  g_wrap_download_item = callback;
-}
-
-void ClearWrapDownloadItem() {
-  g_wrap_download_item.Reset();
-}
-
 // static
 mate::Handle<DownloadItem> DownloadItem::Create(
     v8::Isolate* isolate, content::DownloadItem* item) {
@@ -182,6 +175,18 @@ void* DownloadItem::UserDataKey() {
   return &kDownloadItemSavePathKey;
 }
 
+void ClearWrapDownloadItem() {
+  g_wrap_download_item.Reset();
+}
+
+void SetWrapDownloadItem(const WrapDownloadItemCallback& callback) {
+  g_wrap_download_item = callback;
+
+  // Cleanup the wrapper on exit.
+  atom::AtomBrowserMainParts::Get()->RegisterDestructionCallback(
+      base::Bind(ClearWrapDownloadItem));
+}
+
 }  // namespace api
 
 }  // namespace atom
@@ -193,7 +198,6 @@ void Initialize(v8::Local<v8::Object> exports, v8::Local<v8::Value> unused,
   v8::Isolate* isolate = context->GetIsolate();
   mate::Dictionary dict(isolate, exports);
   dict.SetMethod("_setWrapDownloadItem", &atom::api::SetWrapDownloadItem);
-  dict.SetMethod("_clearWrapDownloadItem", &atom::api::ClearWrapDownloadItem);
 }
 
 }  // namespace
diff --git a/atom/browser/api/atom_api_global_shortcut.cc b/atom/browser/api/atom_api_global_shortcut.cc
index f5a03e4abf90..6ab4fa4b6186 100644
--- a/atom/browser/api/atom_api_global_shortcut.cc
+++ b/atom/browser/api/atom_api_global_shortcut.cc
@@ -23,6 +23,9 @@ GlobalShortcut::GlobalShortcut() {
 }
 
 GlobalShortcut::~GlobalShortcut() {
+}
+
+void GlobalShortcut::Destroy() {
   UnregisterAll();
 }
 
diff --git a/atom/browser/api/atom_api_global_shortcut.h b/atom/browser/api/atom_api_global_shortcut.h
index 15cd3d4e0edb..93eb7853ae0d 100644
--- a/atom/browser/api/atom_api_global_shortcut.h
+++ b/atom/browser/api/atom_api_global_shortcut.h
@@ -8,9 +8,9 @@
 #include <map>
 #include <string>
 
+#include "atom/browser/api/trackable_object.h"
 #include "base/callback.h"
 #include "chrome/browser/extensions/global_shortcut_listener.h"
-#include "native_mate/wrappable.h"
 #include "native_mate/handle.h"
 #include "ui/base/accelerators/accelerator.h"
 
@@ -19,13 +19,16 @@ namespace atom {
 namespace api {
 
 class GlobalShortcut : public extensions::GlobalShortcutListener::Observer,
-                       public mate::Wrappable {
+                       public mate::TrackableObject<GlobalShortcut> {
  public:
   static mate::Handle<GlobalShortcut> Create(v8::Isolate* isolate);
 
  protected:
   GlobalShortcut();
-  virtual ~GlobalShortcut();
+  ~GlobalShortcut() override;
+
+  // mate::TrackableObject:
+  void Destroy() override;
 
   // mate::Wrappable implementations:
   mate::ObjectTemplateBuilder GetObjectTemplateBuilder(
diff --git a/atom/browser/api/atom_api_menu.cc b/atom/browser/api/atom_api_menu.cc
index 9bd724a9612e..1f16a428da01 100644
--- a/atom/browser/api/atom_api_menu.cc
+++ b/atom/browser/api/atom_api_menu.cc
@@ -27,6 +27,14 @@ Menu::Menu()
 Menu::~Menu() {
 }
 
+void Menu::Destroy() {
+  model_.reset();
+}
+
+bool Menu::IsDestroyed() const {
+  return !model_;
+}
+
 void Menu::AfterInit(v8::Isolate* isolate) {
   mate::Dictionary wrappable(isolate, GetWrapper(isolate));
   mate::Dictionary delegate;
diff --git a/atom/browser/api/atom_api_menu.h b/atom/browser/api/atom_api_menu.h
index 0d93c0d46be6..545dd18e386c 100644
--- a/atom/browser/api/atom_api_menu.h
+++ b/atom/browser/api/atom_api_menu.h
@@ -8,16 +8,16 @@
 #include <string>
 
 #include "atom/browser/api/atom_api_window.h"
+#include "atom/browser/api/trackable_object.h"
 #include "atom/browser/ui/atom_menu_model.h"
 #include "base/callback.h"
 #include "base/memory/scoped_ptr.h"
-#include "native_mate/wrappable.h"
 
 namespace atom {
 
 namespace api {
 
-class Menu : public mate::Wrappable,
+class Menu : public mate::TrackableObject<Menu>,
              public AtomMenuModel::Delegate {
  public:
   static mate::Wrappable* Create();
@@ -37,9 +37,13 @@ class Menu : public mate::Wrappable,
 
  protected:
   Menu();
-  virtual ~Menu();
+  ~Menu() override;
+
+  // mate::TrackableObject:
+  void Destroy() override;
 
   // mate::Wrappable:
+  bool IsDestroyed() const override;
   void AfterInit(v8::Isolate* isolate) override;
 
   // ui::SimpleMenuModel::Delegate:
diff --git a/atom/browser/api/atom_api_menu_mac.h b/atom/browser/api/atom_api_menu_mac.h
index 5a086776a639..baa2aff349e1 100644
--- a/atom/browser/api/atom_api_menu_mac.h
+++ b/atom/browser/api/atom_api_menu_mac.h
@@ -19,6 +19,7 @@ class MenuMac : public Menu {
  protected:
   MenuMac();
 
+  void Destroy() override;
   void Popup(Window* window) override;
   void PopupAt(Window* window, int x, int y) override;
 
diff --git a/atom/browser/api/atom_api_menu_mac.mm b/atom/browser/api/atom_api_menu_mac.mm
index 071753218d6a..5936e0439f4f 100644
--- a/atom/browser/api/atom_api_menu_mac.mm
+++ b/atom/browser/api/atom_api_menu_mac.mm
@@ -18,6 +18,11 @@ namespace api {
 MenuMac::MenuMac() {
 }
 
+void MenuMac::Destroy() {
+  menu_controller_.reset();
+  Menu::Destroy();
+}
+
 void MenuMac::Popup(Window* window) {
   NativeWindow* native_window = window->window();
   if (!native_window)
diff --git a/atom/browser/api/atom_api_power_monitor.cc b/atom/browser/api/atom_api_power_monitor.cc
index 31b35e10cea8..eeb9475c2847 100644
--- a/atom/browser/api/atom_api_power_monitor.cc
+++ b/atom/browser/api/atom_api_power_monitor.cc
@@ -19,6 +19,9 @@ PowerMonitor::PowerMonitor() {
 }
 
 PowerMonitor::~PowerMonitor() {
+}
+
+void PowerMonitor::Destroy() {
   base::PowerMonitor::Get()->RemoveObserver(this);
 }
 
diff --git a/atom/browser/api/atom_api_power_monitor.h b/atom/browser/api/atom_api_power_monitor.h
index dcf0906b437f..9303b3ab288f 100644
--- a/atom/browser/api/atom_api_power_monitor.h
+++ b/atom/browser/api/atom_api_power_monitor.h
@@ -5,7 +5,7 @@
 #ifndef ATOM_BROWSER_API_ATOM_API_POWER_MONITOR_H_
 #define ATOM_BROWSER_API_ATOM_API_POWER_MONITOR_H_
 
-#include "atom/browser/api/event_emitter.h"
+#include "atom/browser/api/trackable_object.h"
 #include "base/compiler_specific.h"
 #include "base/power_monitor/power_observer.h"
 #include "native_mate/handle.h"
@@ -14,14 +14,17 @@ namespace atom {
 
 namespace api {
 
-class PowerMonitor : public mate::EventEmitter,
+class PowerMonitor : public mate::TrackableObject<PowerMonitor>,
                      public base::PowerObserver {
  public:
   static v8::Local<v8::Value> Create(v8::Isolate* isolate);
 
  protected:
   PowerMonitor();
-  virtual ~PowerMonitor();
+  ~PowerMonitor() override;
+
+  // mate::TrackableObject:
+  void Destroy() override;
 
   // base::PowerObserver implementations:
   void OnPowerStateChange(bool on_battery_power) override;
diff --git a/atom/browser/api/atom_api_power_save_blocker.cc b/atom/browser/api/atom_api_power_save_blocker.cc
index 58983e6c846a..f77979ae417f 100644
--- a/atom/browser/api/atom_api_power_save_blocker.cc
+++ b/atom/browser/api/atom_api_power_save_blocker.cc
@@ -45,6 +45,11 @@ PowerSaveBlocker::PowerSaveBlocker()
 PowerSaveBlocker::~PowerSaveBlocker() {
 }
 
+void PowerSaveBlocker::Destroy() {
+  power_save_blocker_types_.clear();
+  power_save_blocker_.reset();
+}
+
 void PowerSaveBlocker::UpdatePowerSaveBlocker() {
   if (power_save_blocker_types_.empty()) {
     power_save_blocker_.reset();
diff --git a/atom/browser/api/atom_api_power_save_blocker.h b/atom/browser/api/atom_api_power_save_blocker.h
index 9861f2b0f7cd..e7ce97878ffb 100644
--- a/atom/browser/api/atom_api_power_save_blocker.h
+++ b/atom/browser/api/atom_api_power_save_blocker.h
@@ -7,10 +7,10 @@
 
 #include <map>
 
+#include "atom/browser/api/trackable_object.h"
 #include "base/memory/scoped_ptr.h"
 #include "content/public/browser/power_save_blocker.h"
 #include "native_mate/handle.h"
-#include "native_mate/wrappable.h"
 
 namespace mate {
 class Dictionary;
@@ -20,13 +20,16 @@ namespace atom {
 
 namespace api {
 
-class PowerSaveBlocker : public mate::Wrappable {
+class PowerSaveBlocker : public mate::TrackableObject<PowerSaveBlocker> {
  public:
   static mate::Handle<PowerSaveBlocker> Create(v8::Isolate* isolate);
 
  protected:
   PowerSaveBlocker();
-  virtual ~PowerSaveBlocker();
+  ~PowerSaveBlocker() override;
+
+  // mate::TrackableObject:
+  void Destroy() override;
 
   // mate::Wrappable implementations:
   mate::ObjectTemplateBuilder GetObjectTemplateBuilder(
@@ -48,7 +51,6 @@ class PowerSaveBlocker : public mate::Wrappable {
       std::map<int, content::PowerSaveBlocker::PowerSaveBlockerType>;
   PowerSaveBlockerTypeMap power_save_blocker_types_;
 
-
   DISALLOW_COPY_AND_ASSIGN(PowerSaveBlocker);
 };
 
diff --git a/atom/browser/api/atom_api_session.cc b/atom/browser/api/atom_api_session.cc
index 5bb96710f226..0ec9c05ed84e 100644
--- a/atom/browser/api/atom_api_session.cc
+++ b/atom/browser/api/atom_api_session.cc
@@ -9,9 +9,10 @@
 
 #include "atom/browser/api/atom_api_cookies.h"
 #include "atom/browser/api/atom_api_download_item.h"
-#include "atom/browser/atom_browser_context.h"
 #include "atom/browser/api/atom_api_web_contents.h"
 #include "atom/browser/api/save_page_handler.h"
+#include "atom/browser/atom_browser_context.h"
+#include "atom/browser/atom_browser_main_parts.h"
 #include "atom/common/native_mate_converters/callback.h"
 #include "atom/common/native_mate_converters/gurl_converter.h"
 #include "atom/common/native_mate_converters/file_path_converter.h"
@@ -395,14 +396,18 @@ mate::Handle<Session> Session::FromPartition(
                     static_cast<AtomBrowserContext*>(browser_context.get()));
 }
 
-void SetWrapSession(const WrapSessionCallback& callback) {
-  g_wrap_session = callback;
-}
-
 void ClearWrapSession() {
   g_wrap_session.Reset();
 }
 
+void SetWrapSession(const WrapSessionCallback& callback) {
+  g_wrap_session = callback;
+
+  // Cleanup the wrapper on exit.
+  atom::AtomBrowserMainParts::Get()->RegisterDestructionCallback(
+      base::Bind(ClearWrapSession));
+}
+
 }  // namespace api
 
 }  // namespace atom
@@ -415,7 +420,6 @@ void Initialize(v8::Local<v8::Object> exports, v8::Local<v8::Value> unused,
   mate::Dictionary dict(isolate, exports);
   dict.SetMethod("fromPartition", &atom::api::Session::FromPartition);
   dict.SetMethod("_setWrapSession", &atom::api::SetWrapSession);
-  dict.SetMethod("_clearWrapSession", &atom::api::ClearWrapSession);
 }
 
 }  // namespace
diff --git a/atom/browser/api/atom_api_tray.h b/atom/browser/api/atom_api_tray.h
index dc9302597cf3..9a423f61764f 100644
--- a/atom/browser/api/atom_api_tray.h
+++ b/atom/browser/api/atom_api_tray.h
@@ -8,7 +8,7 @@
 #include <string>
 #include <vector>
 
-#include "atom/browser/api/event_emitter.h"
+#include "atom/browser/api/trackable_object.h"
 #include "atom/browser/ui/tray_icon_observer.h"
 #include "base/memory/scoped_ptr.h"
 
@@ -29,7 +29,7 @@ namespace api {
 
 class Menu;
 
-class Tray : public mate::EventEmitter,
+class Tray : public mate::TrackableObject<Tray>,
              public TrayIconObserver {
  public:
   static mate::Wrappable* New(v8::Isolate* isolate, const gfx::Image& image);
@@ -39,7 +39,7 @@ class Tray : public mate::EventEmitter,
 
  protected:
   explicit Tray(const gfx::Image& image);
-  virtual ~Tray();
+  ~Tray() override;
 
   // TrayIconObserver:
   void OnClicked(const gfx::Rect& bounds, int modifiers) override;
@@ -53,7 +53,9 @@ class Tray : public mate::EventEmitter,
   // mate::Wrappable:
   bool IsDestroyed() const override;
 
-  void Destroy();
+  // mate::TrackableObject:
+  void Destroy() override;
+
   void SetImage(mate::Arguments* args, const gfx::Image& image);
   void SetPressedImage(mate::Arguments* args, const gfx::Image& image);
   void SetToolTip(mate::Arguments* args, const std::string& tool_tip);
diff --git a/atom/browser/api/atom_api_web_contents.cc b/atom/browser/api/atom_api_web_contents.cc
index c329b257a290..5165877d1670 100644
--- a/atom/browser/api/atom_api_web_contents.cc
+++ b/atom/browser/api/atom_api_web_contents.cc
@@ -1124,14 +1124,18 @@ mate::Handle<WebContents> WebContents::Create(
   return handle;
 }
 
-void SetWrapWebContents(const WrapWebContentsCallback& callback) {
-  g_wrap_web_contents = callback;
-}
-
 void ClearWrapWebContents() {
   g_wrap_web_contents.Reset();
 }
 
+void SetWrapWebContents(const WrapWebContentsCallback& callback) {
+  g_wrap_web_contents = callback;
+
+  // Cleanup the wrapper on exit.
+  atom::AtomBrowserMainParts::Get()->RegisterDestructionCallback(
+      base::Bind(ClearWrapWebContents));
+}
+
 }  // namespace api
 
 }  // namespace atom
@@ -1145,7 +1149,6 @@ void Initialize(v8::Local<v8::Object> exports, v8::Local<v8::Value> unused,
   mate::Dictionary dict(isolate, exports);
   dict.SetMethod("create", &atom::api::WebContents::Create);
   dict.SetMethod("_setWrapWebContents", &atom::api::SetWrapWebContents);
-  dict.SetMethod("_clearWrapWebContents", &atom::api::ClearWrapWebContents);
 }
 
 }  // namespace
diff --git a/atom/browser/api/lib/app.coffee b/atom/browser/api/lib/app.coffee
index 18c80dc2b1f4..ba68076177ae 100644
--- a/atom/browser/api/lib/app.coffee
+++ b/atom/browser/api/lib/app.coffee
@@ -11,14 +11,14 @@ wrapSession = (session) ->
   # session is an Event Emitter.
   session.__proto__ = EventEmitter.prototype
 
-wrapDownloadItem = (download_item) ->
-  # download_item is an Event Emitter.
-  download_item.__proto__ = EventEmitter.prototype
+wrapDownloadItem = (downloadItem) ->
+  # downloadItem is an Event Emitter.
+  downloadItem.__proto__ = EventEmitter.prototype
   # Be compatible with old APIs.
-  download_item.url = download_item.getUrl()
-  download_item.filename = download_item.getFilename()
-  download_item.mimeType = download_item.getMimeType()
-  download_item.hasUserGesture = download_item.hasUserGesture()
+  downloadItem.url = downloadItem.getUrl()
+  downloadItem.filename = downloadItem.getFilename()
+  downloadItem.mimeType = downloadItem.getMimeType()
+  downloadItem.hasUserGesture = downloadItem.hasUserGesture()
 
 app.setApplicationMenu = (menu) ->
   require('menu').setApplicationMenu menu
@@ -57,12 +57,9 @@ app.setDataPath = (path) -> @setPath 'userData', path
 app.resolveProxy = -> @defaultSession.resolveProxy.apply @defaultSession, arguments
 app.on 'activate', (event, hasVisibleWindows) -> @emit 'activate-with-no-open-windows' if not hasVisibleWindows
 
-# Session wrapper.
+# Wrappers for native classes.
 sessionBindings._setWrapSession wrapSession
-process.once 'exit', sessionBindings._clearWrapSession
-
 downloadItemBindings._setWrapDownloadItem wrapDownloadItem
-process.once 'exit', downloadItemBindings._clearWrapDownloadItem
 
 # Only one App object pemitted.
 module.exports = app
diff --git a/atom/browser/api/lib/web-contents.coffee b/atom/browser/api/lib/web-contents.coffee
index eab9f1967158..331a561189d7 100644
--- a/atom/browser/api/lib/web-contents.coffee
+++ b/atom/browser/api/lib/web-contents.coffee
@@ -112,7 +112,6 @@ wrapWebContents = (webContents) ->
     @_printToPDF printingSetting, callback
 
 binding._setWrapWebContents wrapWebContents
-process.once 'exit', binding._clearWrapWebContents
 
 module.exports.create = (options={}) ->
   binding.create(options)
diff --git a/atom/browser/atom_browser_main_parts.cc b/atom/browser/atom_browser_main_parts.cc
index 5fae5bfdbedd..041c9bfc8fbe 100644
--- a/atom/browser/atom_browser_main_parts.cc
+++ b/atom/browser/atom_browser_main_parts.cc
@@ -128,11 +128,23 @@ void AtomBrowserMainParts::PostMainMessageLoopStart() {
 void AtomBrowserMainParts::PostMainMessageLoopRun() {
   brightray::BrowserMainParts::PostMainMessageLoopRun();
 
+#if defined(OS_MACOSX)
+  FreeAppDelegate();
+#endif
+
   // Make sure destruction callbacks are called before message loop is
   // destroyed, otherwise some objects that need to be deleted on IO thread
   // won't be freed.
   for (const auto& callback : destruction_callbacks_)
     callback.Run();
+
+  // Destroy JavaScript environment immediately after running destruction
+  // callbacks.
+  gc_timer_.Stop();
+  node_debugger_.reset();
+  atom_bindings_.reset();
+  node_bindings_.reset();
+  js_env_.reset();
 }
 
 }  // namespace atom
diff --git a/atom/browser/atom_browser_main_parts.h b/atom/browser/atom_browser_main_parts.h
index 65b142157dc1..360b1cba1169 100644
--- a/atom/browser/atom_browser_main_parts.h
+++ b/atom/browser/atom_browser_main_parts.h
@@ -46,7 +46,6 @@ class AtomBrowserMainParts : public brightray::BrowserMainParts {
   void PostMainMessageLoopRun() override;
 #if defined(OS_MACOSX)
   void PreMainMessageLoopStart() override;
-  void PostDestroyThreads() override;
 #endif
 
  private:
@@ -56,6 +55,10 @@ class AtomBrowserMainParts : public brightray::BrowserMainParts {
   void HandleShutdownSignals();
 #endif
 
+#if defined(OS_MACOSX)
+  void FreeAppDelegate();
+#endif
+
   // A fake BrowserProcess object that used to feed the source code from chrome.
   scoped_ptr<BrowserProcess> fake_browser_process_;
 
diff --git a/atom/browser/atom_browser_main_parts_mac.mm b/atom/browser/atom_browser_main_parts_mac.mm
index 1de07dfc0e44..42e3100f490e 100644
--- a/atom/browser/atom_browser_main_parts_mac.mm
+++ b/atom/browser/atom_browser_main_parts_mac.mm
@@ -34,7 +34,7 @@ void AtomBrowserMainParts::PreMainMessageLoopStart() {
       setObject:@"NO" forKey:@"NSTreatUnknownArgumentsAsOpen"];
 }
 
-void AtomBrowserMainParts::PostDestroyThreads() {
+void AtomBrowserMainParts::FreeAppDelegate() {
   [[NSApp delegate] release];
   [NSApp setDelegate:nil];
 }