diff --git a/src/atom-environment.coffee b/src/atom-environment.coffee
index 4cb2e5928..68711b260 100644
--- a/src/atom-environment.coffee
+++ b/src/atom-environment.coffee
@@ -655,8 +655,8 @@ class AtomEnvironment extends Model
     return if not @project
 
     @storeWindowBackground()
-    @saveState(true)
     @packages.deactivatePackages()
+    @saveState(true)
     @saveBlobStoreSync()
 
   openInitialEmptyEditorIfNecessary: ->
diff --git a/src/package-manager.coffee b/src/package-manager.coffee
index 636286640..705755af0 100644
--- a/src/package-manager.coffee
+++ b/src/package-manager.coffee
@@ -468,13 +468,12 @@ class PackageManager
     @activationHookEmitter.on(hook, callback)
 
   serialize: ->
-    for pack in @getLoadedPackages()
+    for pack in @getActivePackages()
       @serializePackage(pack)
     @packageStates
 
   serializePackage: (pack) ->
-    if @isPackageActive(pack.name)
-      @setPackageState(pack.name, state) if state = pack.serialize?()
+    @setPackageState(pack.name, state) if state = pack.serialize?()
 
   # Deactivate all packages
   deactivatePackages: ->
@@ -487,7 +486,7 @@ class PackageManager
   # Deactivate the package with the given name
   deactivatePackage: (name) ->
     pack = @getLoadedPackage(name)
-    @serializePackage(pack)
+    @serializePackage(pack) if @isPackageActive(pack.name)
     pack.deactivate()
     delete @activePackages[pack.name]
     delete @activatingPackages[pack.name]