diff --git a/lib/config.js b/lib/config.js
index 08c8825..dc5b5d9 100644
--- a/lib/config.js
+++ b/lib/config.js
@@ -26,7 +26,7 @@ module.exports = class Config {
       throw new Error('[spike constructor] option "root" is required')
     }
     // merges API options into app.js options
-    let allOpts = Object.assign(this.parseAppJs(opts), opts)
+    let allOpts = merge(this.parseAppJs(opts), opts)
     this.transformSpikeOptionsToWebpack(this.validateOpts(allOpts))
     this.project = project
   }
diff --git a/test/app_config.js b/test/app_config.js
index 91bb84c..b108a29 100644
--- a/test/app_config.js
+++ b/test/app_config.js
@@ -13,6 +13,13 @@ test('API config overrides app.js config', (t) => {
   })
 })
 
+test('API config merges properly with app.js config', (t) => {
+  return compileFixture(t, 'app_config', { testing: { bar: 'double override' } }).then(({res}) => {
+    t.truthy(res.stats.compilation.options.testing.baz === 'override')
+    t.truthy(res.stats.compilation.options.testing.bar === 'double override')
+  })
+})
+
 test('throws error for invalid app.js syntax', (t) => {
   return t.throws(() => compileFixture(t, 'app_config_error'), /Error: wow/)
 })
diff --git a/test/fixtures/app_config/app.js b/test/fixtures/app_config/app.js
index 71d4551..4ce9b66 100644
--- a/test/fixtures/app_config/app.js
+++ b/test/fixtures/app_config/app.js
@@ -1,5 +1,7 @@
 module.exports = {
   testing: {
-    foo: 'override'
+    foo: 'override',
+    bar: 'override',
+    baz: 'override'
   }
 }