diff --git a/src/atom-package.coffee b/src/atom-package.coffee
index c9d1ae8cf..0727ffbf8 100644
--- a/src/atom-package.coffee
+++ b/src/atom-package.coffee
@@ -106,11 +106,12 @@ class AtomPackage extends Package
   deactivate: ->
     @unsubscribeFromActivationEvents()
     @deactivateResources()
+    @deactivateConfig()
     @mainModule?.deactivate?()
 
   deactivateConfig: ->
-    @deactivateResources()
     @mainModule?.deactivateConfig?()
+    @configActivated = false
 
   deactivateResources: ->
     syntax.removeGrammar(grammar) for grammar in @grammars