diff --git a/spec/app/root-view-spec.coffee b/spec/app/root-view-spec.coffee
index 261ba087d..d6e948d41 100644
--- a/spec/app/root-view-spec.coffee
+++ b/spec/app/root-view-spec.coffee
@@ -311,25 +311,35 @@ describe "RootView", ->
         expect(rootView.panes.children('.pane').length).toBe 1
         expect(pane1.outerWidth()).toBe rootView.panes.width()
 
-  describe ".activateExtension(extension)", ->
+  describe "extensions", ->
     extension = null
+
     beforeEach ->
       extension =
         name: 'extension'
+        deactivate: ->
         activate: jasmine.createSpy("activate")
         serialize: -> "it worked"
 
-    it "calls activate on the extension", ->
-      rootView.activateExtension(extension)
-      expect(extension.activate).toHaveBeenCalledWith(rootView, undefined)
+    describe "activation", ->
+      it "calls activate on the extension", ->
+        rootView.activateExtension(extension)
+        expect(extension.activate).toHaveBeenCalledWith(rootView, undefined)
 
-    it "calls activate on the extension with its previous state", ->
-      rootView.activateExtension(extension)
-      extension.activate.reset()
+      it "calls activate on the extension with its previous state", ->
+        rootView.activateExtension(extension)
+        extension.activate.reset()
 
-      newRootView = RootView.deserialize(rootView.serialize())
-      newRootView.activateExtension(extension)
-      expect(extension.activate).toHaveBeenCalledWith(newRootView, "it worked")
+        newRootView = RootView.deserialize(rootView.serialize())
+        newRootView.activateExtension(extension)
+        expect(extension.activate).toHaveBeenCalledWith(newRootView, "it worked")
+
+    describe "deactivation", ->
+      it "is deactivated when the rootView is deactivated", ->
+        rootView.activateExtension(extension)
+        spyOn(extension, "deactivate").andCallThrough()
+        rootView.deactivate()
+        expect(extension.deactivate).toHaveBeenCalled()
 
   describe "the file finder", ->
     describe "when the toggle-file-finder event is triggered", ->
diff --git a/src/app/root-view.coffee b/src/app/root-view.coffee
index 73f856f06..754e22903 100644
--- a/src/app/root-view.coffee
+++ b/src/app/root-view.coffee
@@ -88,6 +88,11 @@ class RootView extends View
     @extensions[extension.name] = extension
     extension.activate(this, @extensionStates[extension.name])
 
+  deactivate: ->
+    atom.rootViewStates[$windowNumber] = @serialize()
+    extension.deactivate() for name, extension of @extensions
+    @remove()
+
   open: (path) ->
     buffer = @project.open(path)
 
diff --git a/src/app/window.coffee b/src/app/window.coffee
index fab7f746c..dd2b85fc7 100644
--- a/src/app/window.coffee
+++ b/src/app/window.coffee
@@ -31,8 +31,7 @@ windowAdditions =
     atom.windowOpened this
 
   shutdown: ->
-    @saveRootViewState()
-    @rootView.remove()
+    @rootView.deactivate()
     $(window).unbind('focus')
     $(window).unbind('blur')
     $(window).off('before')
@@ -46,9 +45,6 @@ windowAdditions =
       new RootView {pathToOpen}
     $(@rootViewParentSelector).append @rootView
 
-  saveRootViewState: ->
-    atom.rootViewStates[$windowNumber] = @rootView.serialize()
-
   loadUserConfiguration: ->
     try
       require atom.userConfigurationPath if fs.exists(atom.userConfigurationPath)