diff --git a/packages/cli/src/commands/app/diff.ts b/packages/cli/src/commands/app/diff.ts
new file mode 100644
index 0000000000..a667407f23
--- /dev/null
+++ b/packages/cli/src/commands/app/diff.ts
@@ -0,0 +1,74 @@
+/*
+ * Copyright 2020 Spotify AB
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+import { Command } from 'commander';
+import {
+  diffTemplateFiles,
+  handlers,
+  handleAllFiles,
+  inquirerPromptFunc,
+  makeCheckPromptFunc,
+  yesPromptFunc,
+} from '../../lib/diff';
+import { version } from '../../lib/version';
+
+const fileHandlers = [
+  {
+    patterns: ['packages/app/package.json'],
+    handler: handlers.appPackageJson,
+  },
+  {
+    patterns: [/tsconfig\.json$/],
+    handler: handlers.exactMatch,
+  },
+  {
+    patterns: [
+      /README\.md$/,
+      /\.eslintrc\.js$/,
+      // make sure files in 1st level of src/ and dev/ exist
+      /^packages\/app\/(src|dev)\/[^/]+$/,
+    ],
+    handler: handlers.exists,
+  },
+  {
+    patterns: [
+      'lerna.json',
+      /^src\//,
+      /^patches\//,
+      /^packages\/app\/public\//,
+      /^packages\/app\/cypress/,
+      // Let plugin:diff take care of the plugins
+      /^plugins/,
+      /package\.json$/,
+    ],
+    handler: handlers.skip,
+  },
+];
+
+export default async (cmd: Command) => {
+  let promptFunc = inquirerPromptFunc;
+  let finalize = () => {};
+
+  if (cmd.check) {
+    [promptFunc, finalize] = makeCheckPromptFunc();
+  } else if (cmd.yes) {
+    promptFunc = yesPromptFunc;
+  }
+
+  const templateFiles = await diffTemplateFiles('default-app', { version });
+  await handleAllFiles(fileHandlers, templateFiles, promptFunc);
+  await finalize();
+};
diff --git a/packages/cli/src/index.ts b/packages/cli/src/index.ts
index f02bf6524f..bdd0d3e1f2 100644
--- a/packages/cli/src/index.ts
+++ b/packages/cli/src/index.ts
@@ -39,6 +39,13 @@ const main = (argv: string[]) => {
     .option('--check', 'Enable type checking and linting')
     .action(actionHandler(() => require('./commands/app/serve')));
 
+  program
+    .command('app:diff')
+    .option('--check', 'Fail if changes are required')
+    .option('--yes', 'Apply all changes')
+    .description('Diff an existing app with the creation template')
+    .action(actionHandler(() => require('./commands/app/diff')));
+
   program
     .command('create-plugin')
     .description('Creates a new plugin in the current repository')
@@ -157,7 +164,7 @@ function actionHandler<T extends readonly any[]>(
   };
 }
 
-process.on('unhandledRejection', (rejection) => {
+process.on('unhandledRejection', rejection => {
   if (rejection instanceof Error) {
     exitWithError(rejection);
   } else {
diff --git a/packages/cli/src/lib/diff/handlers.ts b/packages/cli/src/lib/diff/handlers.ts
index 9e46dd92cf..c4efacb198 100644
--- a/packages/cli/src/lib/diff/handlers.ts
+++ b/packages/cli/src/lib/diff/handlers.ts
@@ -22,6 +22,7 @@ class PackageJsonHandler {
   static async handler(
     { path, write, missing, targetContents, templateContents }: FileDiff,
     prompt: PromptFunc,
+    variant?: string,
   ) {
     console.log('Checking package.json');
 
@@ -32,19 +33,33 @@ class PackageJsonHandler {
     const pkg = JSON.parse(templateContents);
     const targetPkg = JSON.parse(targetContents);
 
-    const handler = new PackageJsonHandler(write, prompt, pkg, targetPkg);
+    const handler = new PackageJsonHandler(
+      write,
+      prompt,
+      pkg,
+      targetPkg,
+      variant,
+    );
     await handler.handle();
   }
 
+  static async appHandler(file: FileDiff, prompt: PromptFunc) {
+    return PackageJsonHandler.handler(file, prompt, 'app');
+  }
+
   constructor(
     private readonly writeFunc: WriteFileFunc,
     private readonly prompt: PromptFunc,
     private readonly pkg: any,
     private readonly targetPkg: any,
+    private readonly variant?: string,
   ) {}
 
   async handle() {
     await this.syncField('main');
+    if (this.variant !== 'app') {
+      await this.syncField('main:src');
+    }
     await this.syncField('types');
     await this.syncField('files');
     await this.syncScripts();
@@ -78,7 +93,7 @@ class PackageJsonHandler {
         targetObj[fieldName] = newValue;
         await this.write();
       }
-    } else {
+    } else if (fieldName in obj) {
       if (
         await this.prompt(
           `package.json is missing field ${fullFieldName}, set to ${coloredNewValue}?`,
@@ -95,6 +110,10 @@ class PackageJsonHandler {
     const targetScripts = (this.targetPkg.scripts =
       this.targetPkg.scripts || {});
 
+    if (!pkgScripts) {
+      return;
+    }
+
     for (const key of Object.keys(pkgScripts)) {
       await this.syncField(key, pkgScripts, targetScripts, 'scripts');
     }
@@ -132,7 +151,14 @@ class PackageJsonHandler {
     const targetDeps = (this.targetPkg[fieldName] =
       this.targetPkg[fieldName] || {});
 
+    if (!pkgDeps) {
+      return;
+    }
+
     for (const key of Object.keys(pkgDeps)) {
+      if (this.variant === 'app' && key.startsWith('plugin-')) {
+        continue;
+      }
       await this.syncField(key, pkgDeps, targetDeps, fieldName);
     }
   }
@@ -206,6 +232,7 @@ export const handlers = {
   exists: existsHandler,
   exactMatch: exactMatchHandler,
   packageJson: PackageJsonHandler.handler,
+  appPackageJson: PackageJsonHandler.appHandler,
 };
 
 export async function handleAllFiles(
diff --git a/packages/cli/templates/default-app/packages/app/tsconfig.json b/packages/cli/templates/default-app/packages/app/tsconfig.json
deleted file mode 100644
index 0457810645..0000000000
--- a/packages/cli/templates/default-app/packages/app/tsconfig.json
+++ /dev/null
@@ -1,20 +0,0 @@
-{
-  "extends": "@spotify/web-scripts/config/tsconfig.json",
-  "compilerOptions": {
-    "target": "es5",
-    "lib": ["dom", "dom.iterable", "esnext"],
-    "allowJs": true,
-    "skipLibCheck": true,
-    "esModuleInterop": true,
-    "allowSyntheticDefaultImports": true,
-    "strict": true,
-    "forceConsistentCasingInFileNames": true,
-    "module": "esnext",
-    "moduleResolution": "node",
-    "resolveJsonModule": true,
-    "isolatedModules": true,
-    "jsx": "react",
-    "incremental": false
-  },
-  "include": ["src"]
-}
diff --git a/packages/cli/templates/default-app/plugins/welcome/tsconfig.json b/packages/cli/templates/default-app/plugins/welcome/tsconfig.json
deleted file mode 100644
index 5a3931ffce..0000000000
--- a/packages/cli/templates/default-app/plugins/welcome/tsconfig.json
+++ /dev/null
@@ -1,5 +0,0 @@
-{
-  "extends": "../../tsconfig.json",
-  "include": ["src"],
-  "compilerOptions": {}
-}
diff --git a/packages/cli/templates/default-app/prettier.config.js b/packages/cli/templates/default-app/prettier.config.js
deleted file mode 100644
index 93df970dd6..0000000000
--- a/packages/cli/templates/default-app/prettier.config.js
+++ /dev/null
@@ -1 +0,0 @@
-module.exports = require('@spotify/web-scripts/config/prettier.config.js');