diff --git a/package.json b/package.json
index 194dcb847..915d1b33f 100644
--- a/package.json
+++ b/package.json
@@ -51,7 +51,7 @@
     "reactionary-atom-fork": "^1.0.0",
     "runas": "1.0.1",
     "scandal": "1.0.3",
-    "scoped-property-store": "^0.14.0",
+    "scoped-property-store": "^0.15.0",
     "scrollbar-style": "^1.0.2",
     "season": "^1.0.2",
     "semver": "2.2.1",
diff --git a/spec/config-spec.coffee b/spec/config-spec.coffee
index cdd071091..e46585d6e 100644
--- a/spec/config-spec.coffee
+++ b/spec/config-spec.coffee
@@ -1075,6 +1075,13 @@ describe "Config", ->
           atom.config.setDefaults("foo", hasDefault: 'ok')
           expect(atom.config.get([".source.coffee", ".string.quoted.single"], "foo.hasDefault")).toBe 'ok'
 
+      describe 'setting priority', ->
+        describe 'when package settings are added after user settings', ->
+          it "returns the user's setting because the user's setting has higher priority", ->
+            atom.config.set(".source.coffee", "foo.bar.baz", 100)
+            atom.config.addScopedSettings("some-package", ".source.coffee", foo: bar: baz: 1)
+            expect(atom.config.get([".source.coffee"], "foo.bar.baz")).toBe 100
+
     describe ".set(scope, keyPath, value)", ->
       it "sets the value and overrides the others", ->
         atom.config.addScopedSettings("config", ".source.coffee .string.quoted.double.coffee", foo: bar: baz: 42)
diff --git a/src/config.coffee b/src/config.coffee
index 163116f71..0983fa966 100644
--- a/src/config.coffee
+++ b/src/config.coffee
@@ -314,6 +314,7 @@ class Config
     @settings = {}
     @scopedSettingsStore = new ScopedPropertyStore
     @usersScopedSettings = new CompositeDisposable
+    @usersScopedSettingPriority = {priority: 1000}
     @configFileHasErrors = false
     @configFilePath = fs.resolve(@configDirPath, 'config', ['json', 'cson'])
     @configFilePath ?= path.join(@configDirPath, 'config.cson')
@@ -537,7 +538,7 @@ class Config
       settings = @scopedSettingsStore.propertiesForSourceAndSelector('user-config', scopeSelector)
       @scopedSettingsStore.removePropertiesForSourceAndSelector('user-config', scopeSelector)
       _.setValueForKeyPath(settings, keyPath, undefined)
-      @addScopedSettings('user-config', scopeSelector, settings)
+      @addScopedSettings('user-config', scopeSelector, settings, @usersScopedSettingPriority)
       @save() unless @configFileHasErrors
       @getDefault(scopeSelector, keyPath)
     else
@@ -881,13 +882,13 @@ class Config
   resetUserScopedSettings: (newScopedSettings) ->
     @usersScopedSettings?.dispose()
     @usersScopedSettings = new CompositeDisposable
-    @usersScopedSettings.add @scopedSettingsStore.addProperties('user-config', newScopedSettings)
+    @usersScopedSettings.add @scopedSettingsStore.addProperties('user-config', newScopedSettings, @usersScopedSettingPriority)
     @emitter.emit 'did-change'
 
-  addScopedSettings: (source, selector, value) ->
+  addScopedSettings: (source, selector, value, options) ->
     settingsBySelector = {}
     settingsBySelector[selector] = value
-    disposable = @scopedSettingsStore.addProperties(source, settingsBySelector)
+    disposable = @scopedSettingsStore.addProperties(source, settingsBySelector, options)
     @emitter.emit 'did-change'
     new Disposable =>
       disposable.dispose()
@@ -901,7 +902,7 @@ class Config
 
     settingsBySelector = {}
     settingsBySelector[selector] = value
-    @usersScopedSettings.add @scopedSettingsStore.addProperties('user-config', settingsBySelector)
+    @usersScopedSettings.add @scopedSettingsStore.addProperties('user-config', settingsBySelector, @usersScopedSettingPriority)
     @emitter.emit 'did-change'
 
   getRawScopedValue: (scopeDescriptor, keyPath) ->