diff --git a/lib/gitWorkflow.js b/lib/gitWorkflow.js
index ac178163c..0674831b9 100644
--- a/lib/gitWorkflow.js
+++ b/lib/gitWorkflow.js
@@ -14,6 +14,23 @@ const STASH = 'lint-staged automatic backup'
 
 const gitApplyArgs = ['apply', '-v', '--whitespace=nowarn', '--recount', '--unidiff-zero']
 
+/**
+ * Delete untracked files using `git clean`
+ * @param {Function} execGit function for executing git commands using execa
+ * @returns {Promise<void>}
+ */
+const cleanUntrackedFiles = async execGit => {
+  const untrackedFiles = await execGit(['ls-files', '--others', '--exclude-standard'])
+  if (untrackedFiles) {
+    debug('Detected unstaged, untracked files: ', untrackedFiles)
+    debug(
+      'This is probably due to a bug in git =< 2.13.0 where `git stash --keep-index` resurrects deleted files.'
+    )
+    debug('Deleting the files using `git clean`...')
+    await execGit(['clean', '--force', untrackedFiles.split('\n').join(' ')])
+  }
+}
+
 class GitWorkflow {
   constructor({ gitDir, stagedFileChunks }) {
     this.execGit = (args, options = {}) => execGit(args, { ...options, cwd: gitDir })
@@ -69,18 +86,15 @@ class GitWorkflow {
       debug('Done backing up merge state!')
     }
 
-    // Get diff of staged modifications. This will be applied back to the index. after stashing all changes.
-    // The `git stash save --keep-index` option cannot be used since it resurrects deleted files on
-    // git versions before v2.23.0 (https://github.com/git/git/blob/master/Documentation/RelNotes/2.23.0.txt#L322)
-    const stagedDiff = await this.execGit(['diff', '--binary', '--cached'])
-
     // Save stash of entire original state, including unstaged and untracked changes.
-    // This should remove all changes from the index.
-    await this.execGit(['stash', 'save', '--quiet', '--include-untracked', STASH])
+    // `--keep-index leaves only staged files on disk, for tasks.`
+    await this.execGit(['stash', 'save', '--quiet', '--include-untracked', '--keep-index', STASH])
 
-    // Apply staged modifications back to the index
-    await this.execGit([...gitApplyArgs, '--index'], { input: `${stagedDiff}\n` })
+    // There is a bug in git =< 2.13.0 where `--keep-index` resurrects deleted files.
+    // These files should be listed and deleted before proceeding.
+    await cleanUntrackedFiles(this.execGit)
 
+    // Get a diff of unstaged changes by saved stash against what's left on disk.
     this.unstagedDiff = await this.execGit([
       'diff',
       '--binary',
@@ -91,6 +105,7 @@ class GitWorkflow {
       await this.getBackupStash(),
       '-R' // Show diff in reverse
     ])
+
     debug('Done backing up original state!')
   }
 
@@ -189,3 +204,4 @@ class GitWorkflow {
 }
 
 module.exports = GitWorkflow
+module.exports.cleanUntrackedFiles = cleanUntrackedFiles
diff --git a/test/gitWorkflow.spec.js b/test/gitWorkflow.spec.js
new file mode 100644
index 000000000..f52a0af81
--- /dev/null
+++ b/test/gitWorkflow.spec.js
@@ -0,0 +1,77 @@
+import fs from 'fs-extra'
+import normalize from 'normalize-path'
+import os from 'os'
+import path from 'path'
+import nanoid from 'nanoid'
+
+import execGitBase from '../lib/execGit'
+import { cleanUntrackedFiles } from '../lib/gitWorkflow'
+
+jest.unmock('execa')
+
+jest.setTimeout(20000)
+
+const isAppveyor = !!process.env.APPVEYOR
+const osTmpDir = isAppveyor ? 'C:\\projects' : fs.realpathSync(os.tmpdir())
+
+/**
+ * Create temporary directory and return its path
+ * @returns {Promise<String>}
+ */
+const createTempDir = async () => {
+  const dirname = path.resolve(osTmpDir, 'lint-staged-test', nanoid())
+  await fs.ensureDir(dirname)
+  return dirname
+}
+
+/**
+ * Remove temporary directory
+ * @param {String} dirname
+ * @returns {Promise<Void>}
+ */
+const removeTempDir = async dirname => {
+  await fs.remove(dirname)
+}
+
+let tmpDir, cwd
+
+/** Append to file, creating if it doesn't exist */
+const appendFile = async (filename, content, dir = cwd) =>
+  fs.appendFile(path.resolve(dir, filename), content)
+
+/** Wrap execGit to always pass `gitOps` */
+const execGit = async args => execGitBase(args, { cwd })
+
+/** Initialize git repo for test */
+const initGitRepo = async () => {
+  await execGit('init')
+  await execGit(['config', 'user.name', '"test"'])
+  await execGit(['config', 'user.email', '"test@test.com"'])
+  await appendFile('README.md', '# Test\n')
+  await execGit(['add', 'README.md'])
+  await execGit(['commit', '-m initial commit'])
+}
+
+describe('gitWorkflow', () => {
+  beforeEach(async () => {
+    tmpDir = await createTempDir()
+    cwd = normalize(tmpDir)
+    await initGitRepo()
+  })
+
+  afterEach(async () => {
+    if (!isAppveyor) {
+      await removeTempDir(tmpDir)
+    }
+  })
+
+  describe('cleanUntrackedFiles', () => {
+    it('should delete untracked, unstaged files', async () => {
+      const testFile = path.resolve(cwd, 'test.js')
+      await appendFile(testFile, 'test')
+      expect(await fs.exists(testFile)).toEqual(true)
+      await cleanUntrackedFiles(execGit)
+      expect(await fs.exists(testFile)).toEqual(false)
+    })
+  })
+})
diff --git a/test/runAll.unmocked.spec.js b/test/runAll.unmocked.spec.js
index 52c6f9078..6c14c310e 100644
--- a/test/runAll.unmocked.spec.js
+++ b/test/runAll.unmocked.spec.js
@@ -55,15 +55,15 @@ let cwd
 
 // Get file content
 const readFile = async (filename, dir = cwd) =>
-  fs.readFile(path.join(dir, filename), { encoding: 'utf-8' })
+  fs.readFile(path.resolve(dir, filename), { encoding: 'utf-8' })
 
 // Append to file, creating if it doesn't exist
 const appendFile = async (filename, content, dir = cwd) =>
-  fs.appendFile(path.join(dir, filename), content)
+  fs.appendFile(path.resolve(dir, filename), content)
 
 // Write (over) file, creating if it doesn't exist
 const writeFile = async (filename, content, dir = cwd) =>
-  fs.writeFile(path.join(dir, filename), content)
+  fs.writeFile(path.resolve(dir, filename), content)
 
 // Wrap execGit to always pass `gitOps`
 const execGit = async args => execGitBase(args, { cwd })