diff --git a/spec/package-manager-spec.coffee b/spec/package-manager-spec.coffee
index b4b89314e..3015aa786 100644
--- a/spec/package-manager-spec.coffee
+++ b/spec/package-manager-spec.coffee
@@ -502,6 +502,7 @@ describe "PackageManager", ->
       runs ->
         expect(pack.mainModule.someNumber).not.toBe 77
         pack.mainModule.someNumber = 77
+        atom.packages.serializePackage("package-with-serialization")
         atom.packages.deactivatePackage("package-with-serialization")
         spyOn(pack.mainModule, 'activate').andCallThrough()
       waitsForPromise ->
@@ -899,6 +900,22 @@ describe "PackageManager", ->
         expect(atom.packages.packageStates['package-with-serialization']).toEqual someNumber: 1
         expect(console.error).toHaveBeenCalled()
 
+  describe "::deactivatePackages()", ->
+    it "deactivates all packages but does not serialize them", ->
+      [pack1, pack2] = []
+
+      waitsForPromise ->
+        atom.packages.activatePackage("package-with-deactivate").then (p) -> pack1 = p
+        atom.packages.activatePackage("package-with-serialization").then (p) -> pack2 = p
+
+      runs ->
+        spyOn(pack1.mainModule, 'deactivate')
+        spyOn(pack2.mainModule, 'serialize')
+        atom.packages.deactivatePackages()
+
+        expect(pack1.mainModule.deactivate).toHaveBeenCalled()
+        expect(pack2.mainModule.serialize).not.toHaveBeenCalled()
+
   describe "::deactivatePackage(id)", ->
     afterEach ->
       atom.packages.unloadPackages()
diff --git a/src/package-manager.coffee b/src/package-manager.coffee
index 8f2924358..a2e792e26 100644
--- a/src/package-manager.coffee
+++ b/src/package-manager.coffee
@@ -486,15 +486,15 @@ class PackageManager
   # Deactivate all packages
   deactivatePackages: ->
     @config.transact =>
-      @deactivatePackage(pack.name) for pack in @getLoadedPackages()
+      @deactivatePackage(pack.name, true) for pack in @getLoadedPackages()
       return
     @unobserveDisabledPackages()
     @unobservePackagesWithKeymapsDisabled()
 
   # Deactivate the package with the given name
-  deactivatePackage: (name) ->
+  deactivatePackage: (name, suppressSerialization) ->
     pack = @getLoadedPackage(name)
-    @serializePackage(pack) if @isPackageActive(pack.name)
+    @serializePackage(pack) if not suppressSerialization and @isPackageActive(pack.name)
     pack.deactivate()
     delete @activePackages[pack.name]
     delete @activatingPackages[pack.name]