diff --git a/spec/app/config-spec.coffee b/spec/app/config-spec.coffee
index 63dfac4ae..b42f140f5 100644
--- a/spec/app/config-spec.coffee
+++ b/spec/app/config-spec.coffee
@@ -1,3 +1,5 @@
+fs = require 'fs'
+
 describe "Config", ->
   describe ".get(keyPath) and .set(keyPath, value)", ->
     it "allows a key path's value to be read and written", ->
@@ -15,14 +17,33 @@ describe "Config", ->
       expect(config.save).toHaveBeenCalled()
       expect(observeHandler).toHaveBeenCalledWith 42
 
+  describe ".save()", ->
+    beforeEach ->
+      spyOn(fs, 'write')
+      jasmine.unspy config, 'save'
+
+    it "writes any non-default properties to the config.json in the user's .atom directory", ->
+      config.set("a.b.c", 1)
+      config.set("a.b.d", 2)
+      config.set("x.y.z", 3)
+      config.setDefaults("a.b", e: 4, f: 5)
+
+      config.save()
+
+      writtenConfig = JSON.parse(fs.write.argsForCall[0][1])
+      expect(writtenConfig).toEqual config.settings
+
   describe ".setDefaults(keyPath, defaults)", ->
     it "assigns any previously-unassigned keys to the object at the key path", ->
       config.set("foo.bar.baz", a: 1)
       config.setDefaults("foo.bar.baz", a: 2, b: 3, c: 4)
-      expect(config.get("foo.bar.baz")).toEqual(a: 1, b: 3, c: 4)
+      expect(config.get("foo.bar.baz.a")).toBe 1
+      expect(config.get("foo.bar.baz.b")).toBe 3
+      expect(config.get("foo.bar.baz.c")).toBe 4
 
       config.setDefaults("foo.quux", x: 0, y: 1)
-      expect(config.get("foo.quux")).toEqual(x: 0, y: 1)
+      expect(config.get("foo.quux.x")).toBe 0
+      expect(config.get("foo.quux.y")).toBe 1
 
   describe ".update()", ->
     it "updates observers if a value is mutated without the use of .set", ->
diff --git a/src/app/config.coffee b/src/app/config.coffee
index fca996949..d006e7540 100644
--- a/src/app/config.coffee
+++ b/src/app/config.coffee
@@ -22,12 +22,14 @@ class Config
   configDirPath: configDirPath
   themeDirPaths: [userThemesDirPath, bundledThemesDirPath]
   packageDirPaths: [userPackagesDirPath, bundledVendorPackagesDirPath, bundledPackagesDirPath]
+  defaultSettings: null
   settings: null
 
   constructor: ->
-    @settings =
+    @defaultSettings =
       core: _.clone(require('root-view').configDefaults)
       editor: _.clone(require('editor').configDefaults)
+    @settings = {}
 
   load: ->
     @loadUserConfig()
@@ -41,7 +43,8 @@ class Config
       _.extend(@settings, userConfig)
 
   get: (keyPath) ->
-    _.valueForKeyPath(@settings, keyPath)
+    _.valueForKeyPath(@settings, keyPath) ?
+      _.valueForKeyPath(@defaultSettings, keyPath)
 
   set: (keyPath, value) ->
     keys = keyPath.split('.')
@@ -57,12 +60,12 @@ class Config
 
   setDefaults: (keyPath, defaults) ->
     keys = keyPath.split('.')
-    hash = @settings
+    hash = @defaultSettings
     for key in keys
       hash[key] ?= {}
       hash = hash[key]
 
-    _.defaults hash, defaults
+    _.extend hash, defaults
     @update()
 
   observe: (keyPath, callback) ->