diff --git a/packages/@vue/cli-service/lib/Service.js b/packages/@vue/cli-service/lib/Service.js
index 525da990c..9be1aa96d 100644
--- a/packages/@vue/cli-service/lib/Service.js
+++ b/packages/@vue/cli-service/lib/Service.js
@@ -25,7 +25,10 @@ module.exports = class Service {
     this.loadEnv()
 
     const userOptions = this.loadProjectOptions(projectOptions)
-    this.projectOptions = Object.assign(defaults(), userOptions)
+    const defaultOptions = defaults()
+    this.projectOptions = Object.assign({}, defaultOptions, userOptions, {
+      vueLoader: Object.assign(defaultOptions.vueLoader, userOptions.vueLoader)
+    })
 
     debug('vue:project-config')(this.projectOptions)
 
diff --git a/packages/@vue/cli-service/lib/options.js b/packages/@vue/cli-service/lib/options.js
index 0100ce733..1e74f7277 100644
--- a/packages/@vue/cli-service/lib/options.js
+++ b/packages/@vue/cli-service/lib/options.js
@@ -55,7 +55,12 @@ exports.defaults = () => ({
   compiler: false,
 
   // vue-loader options
-  vueLoader: {},
+  vueLoader: {
+    template: {
+      // for pug
+      doctype: 'html'
+    }
+  },
 
   // sourceMap for production build?
   productionSourceMap: true,