diff --git a/packages/cli/src/commands/init/__tests__/template.test.js b/packages/cli/src/commands/init/__tests__/template.test.js
index 3af48b748..fc41fdce0 100644
--- a/packages/cli/src/commands/init/__tests__/template.test.js
+++ b/packages/cli/src/commands/init/__tests__/template.test.js
@@ -72,7 +72,9 @@ test('copyTemplate', async () => {
     TEMPLATE_NAME,
     TEMPLATE_DIR,
   );
-  expect(copyFiles.default).toHaveBeenCalledWith(expect.any(String), CWD);
+  expect(copyFiles.default).toHaveBeenCalledWith(expect.any(String), CWD, {
+    exclude: [expect.any(RegExp)],
+  });
 });
 
 test('executePostInitScript', async () => {
diff --git a/packages/cli/src/commands/init/template.js b/packages/cli/src/commands/init/template.js
index 8e2f9dede..918a40be6 100644
--- a/packages/cli/src/commands/init/template.js
+++ b/packages/cli/src/commands/init/template.js
@@ -54,7 +54,9 @@ export async function copyTemplate(
 
   logger.debug(`Copying template from ${templatePath}`);
 
-  await copyFiles(templatePath, process.cwd());
+  await copyFiles(templatePath, process.cwd(), {
+    exclude: [new RegExp(path.resolve(templatePath, 'node_modules'))],
+  });
 }
 
 export function executePostInitScript(
diff --git a/packages/cli/src/tools/__tests__/__fixtures__/binary.keystore b/packages/cli/src/tools/__tests__/__fixtures__/binary.keystore
new file mode 100644
index 000000000..364e105ed
Binary files /dev/null and b/packages/cli/src/tools/__tests__/__fixtures__/binary.keystore differ
diff --git a/packages/cli/src/tools/__tests__/__fixtures__/extraDir/file3 b/packages/cli/src/tools/__tests__/__fixtures__/extraDir/file3
new file mode 100644
index 000000000..e69de29bb
diff --git a/packages/cli/src/tools/__tests__/__fixtures__/file1.js b/packages/cli/src/tools/__tests__/__fixtures__/file1.js
new file mode 100644
index 000000000..bd816eaba
--- /dev/null
+++ b/packages/cli/src/tools/__tests__/__fixtures__/file1.js
@@ -0,0 +1 @@
+module.exports = 1;
diff --git a/packages/cli/src/tools/__tests__/__fixtures__/file2.txt b/packages/cli/src/tools/__tests__/__fixtures__/file2.txt
new file mode 100644
index 000000000..6c493ff74
--- /dev/null
+++ b/packages/cli/src/tools/__tests__/__fixtures__/file2.txt
@@ -0,0 +1 @@
+file2
diff --git a/packages/cli/src/tools/__tests__/copyFiles.test.js b/packages/cli/src/tools/__tests__/copyFiles.test.js
new file mode 100644
index 000000000..477d4721d
--- /dev/null
+++ b/packages/cli/src/tools/__tests__/copyFiles.test.js
@@ -0,0 +1,61 @@
+// @flow
+import fs from 'fs';
+import path from 'path';
+import copyFiles from '../copyFiles';
+import {cleanup, getTempDirectory} from '../../../../../jest/helpers';
+
+const DIR = getTempDirectory('copyFiles-test');
+
+beforeEach(() => {
+  cleanup(DIR);
+  fs.mkdirSync(DIR);
+});
+
+afterEach(() => {
+  cleanup(DIR);
+});
+
+test('copies text and binary files from source to destination', async () => {
+  const src = path.resolve(__dirname, './__fixtures__');
+  await copyFiles(src, DIR);
+
+  expect(fs.readdirSync(DIR)).toMatchInlineSnapshot(`
+    Array [
+      "binary.keystore",
+      "extraDir",
+      "file1.js",
+      "file2.txt",
+    ]
+  `);
+
+  ['binary.keystore', 'file1.js', 'file2.txt'].forEach(file => {
+    expect(fs.readFileSync(path.join(src, file))).toEqual(
+      fs.readFileSync(path.join(DIR, file)),
+    );
+  });
+
+  expect(fs.readdirSync(path.join(DIR, 'extraDir'))).toMatchInlineSnapshot(`
+    Array [
+      "file3",
+    ]
+  `);
+
+  expect(fs.readFileSync(path.join(src, 'extraDir', 'file3'))).toEqual(
+    fs.readFileSync(path.join(DIR, 'extraDir', 'file3')),
+  );
+});
+
+test('copies files from source to destination excluding directory', async () => {
+  const src = path.resolve(__dirname, './__fixtures__');
+  await copyFiles(src, DIR, {
+    exclude: [new RegExp(path.join(src, 'extraDir'))],
+  });
+
+  expect(fs.readdirSync(DIR)).toMatchInlineSnapshot(`
+    Array [
+      "binary.keystore",
+      "file1.js",
+      "file2.txt",
+    ]
+  `);
+});
diff --git a/packages/cli/src/tools/copyFiles.js b/packages/cli/src/tools/copyFiles.js
index 6f8206a05..e2e5fad66 100644
--- a/packages/cli/src/tools/copyFiles.js
+++ b/packages/cli/src/tools/copyFiles.js
@@ -11,12 +11,24 @@ import fs from 'fs';
 import path from 'path';
 import walk from './walk';
 
+type Options = {
+  exclude?: Array<RegExp>,
+};
+
 /**
  * Copy files (binary included) recursively.
  */
-async function copyFiles(srcPath: string, destPath: string) {
+async function copyFiles(
+  srcPath: string,
+  destPath: string,
+  options?: Options = {},
+) {
   return Promise.all(
     walk(srcPath).map(async absoluteSrcFilePath => {
+      const exclude = options.exclude;
+      if (exclude && exclude.some(p => p.test(absoluteSrcFilePath))) {
+        return;
+      }
       const relativeFilePath = path.relative(srcPath, absoluteSrcFilePath);
       await copyFile(
         absoluteSrcFilePath,