diff --git a/spec/app/root-view-spec.coffee b/spec/app/root-view-spec.coffee
index ca5f85302..0b7399c4e 100644
--- a/spec/app/root-view-spec.coffee
+++ b/spec/app/root-view-spec.coffee
@@ -397,6 +397,14 @@ describe "RootView", ->
         expect(-> rootView.activateExtension({ activate: -> })).toThrow()
 
     describe "deactivation", ->
+      it "is deactivated and removed from the extension list", ->
+        rootView.activateExtension(extension)
+        expect(rootView.extensions[extension.name]).toBeTruthy()
+        spyOn(extension, "deactivate").andCallThrough()
+        rootView.deactivateExtension(extension)
+        expect(extension.deactivate).toHaveBeenCalled()
+        expect(rootView.extensions[extension.name]).toBeFalsy()
+
       it "is deactivated when the rootView is deactivated", ->
         rootView.activateExtension(extension)
         spyOn(extension, "deactivate").andCallThrough()
diff --git a/spec/extensions/tree-view-spec.coffee b/spec/extensions/tree-view-spec.coffee
index 1d1b1bfab..57270c98a 100644
--- a/spec/extensions/tree-view-spec.coffee
+++ b/spec/extensions/tree-view-spec.coffee
@@ -80,7 +80,7 @@ describe "TreeView", ->
   describe "when the prototypes deactivate method is called", ->
     it "calls the deactivate on tree view instance", ->
       spyOn(treeView, "deactivate").andCallThrough()
-      TreeView.deactivate()
+      rootView.deactivateExtension(TreeView)
       expect(treeView.deactivate).toHaveBeenCalled()
 
     it "restores expanded directories and selected file when deserialized", ->
diff --git a/src/app/root-view.coffee b/src/app/root-view.coffee
index ac117aeb9..1364320e9 100644
--- a/src/app/root-view.coffee
+++ b/src/app/root-view.coffee
@@ -87,6 +87,10 @@ class RootView extends View
     @extensions[extension.name] = extension
     extension.activate(this, @extensionStates[extension.name])
 
+  deactivateExtension: (extension) ->
+    extension.deactivate?()
+    delete @extensions[extension.name]
+
   deactivate: ->
     atom.rootViewStates[$windowNumber] = JSON.stringify(@serialize())
     extension.deactivate?() for name, extension of @extensions