diff --git a/bin/cli b/bin/cli
index 5e3641fefc..7d84ec0d2f 100755
--- a/bin/cli
+++ b/bin/cli
@@ -1,7 +1,9 @@
 #!/usr/bin/env node
 
 const fs = require('fs-extra')
+const os = require('os')
 const path = require('path')
+
 const { exec } = require('../lib/exec')
 const { runUpgrade } = require('../lib/upgradeToV13')
 
@@ -29,6 +31,14 @@ public/
 .idea
 `
 
+const packageJson = {
+  scripts: {
+    start: 'govuk-prototype-kit start'
+  }
+}
+
+const packageJsonFormat = { encoding: 'utf8', EOL: os.EOL, spaces: 2 }
+
 function usage () {
   const prog = 'npx govuk-prototype-kit'
   console.log(`
@@ -84,34 +94,73 @@ const getChosenKitDependency = () => {
 
 (async () => {
   if (command === 'create') {
+    // Install as a two-stage bootstrap process.
+    //
+    // In stage one (`create`) we create an empty project folder and install
+    // govuk-prototype-kit and govuk-frontend, then bootstrap stage two from
+    // the newly installed package.
+    //
+    // In stage two (`init`) we do the actual setup of the starter files.
+    //
+    // Doing it this way means we can be sure the version of the cli matches
+    // the version of the kit the user ends up with. Try to put as much logic
+    // as possible into stage two; stage one should ideally be able to install
+    // any future version of the kit.
+
     const installDirectory = getInstallLocation()
     const kitDependency = getChosenKitDependency()
 
-    const copyFile = (fileName) => fs.copy(path.join(kitRoot, fileName), path.join(installDirectory, fileName))
-
     await fs.ensureDir(installDirectory)
     if ((await fs.readdir(installDirectory)).length > 0) {
       console.error(`Directory ${installDirectory} is not empty, please specify an empty location.`)
-      process.exit(3)
+      process.exitCode = 3
+      return
     }
 
-    await Promise.all([
-      fs.copy(path.join(kitRoot, 'prototype-starter'), installDirectory),
-      fs.writeFile(path.join(installDirectory, '.gitignore'), gitignore, 'utf8'),
-      fs.writeFile(path.join(installDirectory, '.npmrc'), npmrc, 'utf8'),
-      copyFile('LICENCE.txt')
-    ])
+    await fs.writeJson(path.join(installDirectory, 'package.json'), {}, packageJsonFormat)
 
     console.log('Creating your prototype')
     const dots = setInterval(() => {
       process.stdout.write('.')
     }, 500)
+
     await exec(`npm install ${kitDependency} govuk-frontend`, {
       stdio: 'inherit',
       cwd: installDirectory
     }, console.log)
+
     clearInterval(dots)
 
+    await exec(`npx govuk-prototype-kit init -- ${installDirectory}`, {
+      stdio: 'inherit',
+      cwd: installDirectory
+    }, console.log)
+  } else if (command === 'init') {
+    // `init` is stage two of the install process (see above), it should be
+    // called by `create` with the correct arguments.
+
+    if (additionalOptions[0] !== '--') {
+      usage()
+      process.exitCode = 2
+      return
+    }
+
+    const installDirectory = additionalOptions[1]
+
+    const copyFile = (fileName) => fs.copy(path.join(kitRoot, fileName), path.join(installDirectory, fileName))
+    const updatePackageJson = async (packageJsonPath) => {
+      let newPackageJson = Object.assign({}, packageJson)
+      newPackageJson = Object.assign(newPackageJson, await fs.readJson(packageJsonPath))
+      await fs.writeJson(packageJsonPath, newPackageJson, packageJsonFormat)
+    }
+
+    await Promise.all([
+      fs.copy(path.join(kitRoot, 'prototype-starter'), installDirectory),
+      fs.writeFile(path.join(installDirectory, '.gitignore'), gitignore, 'utf8'),
+      fs.writeFile(path.join(installDirectory, '.npmrc'), npmrc, 'utf8'),
+      copyFile('LICENCE.txt'),
+      updatePackageJson(path.join(installDirectory, 'package.json'))
+    ])
   } else if (command === 'start') {
     require('../start')
   } else if (command === 'upgrade') {
diff --git a/package.json b/package.json
index 20aee3460a..ecab3c3305 100644
--- a/package.json
+++ b/package.json
@@ -27,7 +27,7 @@
     "tmp-kit": "mkdir -p $TMPDIR/govuk-prototype-kit-playground && cd $TMPDIR/govuk-prototype-kit-playground && rm -Rf ./* && govuk-prototype-kit create --version local . && npm start",
     "start": "echo 'This project cannot be started, in order to test this project please create a prototype kit using the cli.'",
     "start:package": "KIT_TEST_DIR=tmp/test-prototype-package node cypress/scripts/run-starter-prototype",
-    "lint": "standard '**/*.js' scripts/create-release-archive scripts/cli lib/build/dev-server lib/build/generate-assets",
+    "lint": "standard '**/*.js' bin/cli scripts/create-release-archive lib/build/dev-server lib/build/generate-assets",
     "rapidtest": "jest --bail",
     "cypress:open": "cypress open",
     "test:heroku": "echo 'test:heroku' needs to be implemented",
diff --git a/prototype-starter/package.json b/prototype-starter/package.json
deleted file mode 100644
index 4297742a10..0000000000
--- a/prototype-starter/package.json
+++ /dev/null
@@ -1,5 +0,0 @@
-{
-  "scripts": {
-    "start": "govuk-prototype-kit start"
-  }
-}