diff --git a/lib/gitWorkflow.js b/lib/gitWorkflow.js
index 128a96b13..ac178163c 100644
--- a/lib/gitWorkflow.js
+++ b/lib/gitWorkflow.js
@@ -15,18 +15,19 @@ const STASH = 'lint-staged automatic backup'
 const gitApplyArgs = ['apply', '-v', '--whitespace=nowarn', '--recount', '--unidiff-zero']
 
 class GitWorkflow {
-  constructor(cwd) {
-    this.execGit = (args, options = {}) => execGit(args, { ...options, cwd })
+  constructor({ gitDir, stagedFileChunks }) {
+    this.execGit = (args, options = {}) => execGit(args, { ...options, cwd: gitDir })
     this.unstagedDiff = null
-    this.cwd = cwd
+    this.gitDir = gitDir
+    this.stagedFileChunks = stagedFileChunks
 
     /**
      * These three files hold state about an ongoing git merge
      * Resolve paths during constructor
      */
-    this.mergeHeadFile = path.resolve(this.cwd, '.git', MERGE_HEAD)
-    this.mergeModeFile = path.resolve(this.cwd, '.git', MERGE_MODE)
-    this.mergeMsgFile = path.resolve(this.cwd, '.git', MERGE_MSG)
+    this.mergeHeadFile = path.resolve(this.gitDir, '.git', MERGE_HEAD)
+    this.mergeModeFile = path.resolve(this.gitDir, '.git', MERGE_MODE)
+    this.mergeMsgFile = path.resolve(this.gitDir, '.git', MERGE_MSG)
   }
 
   /**
@@ -107,7 +108,11 @@ class GitWorkflow {
       debug('Detected files modified by tasks:')
       debug(modifiedFiles)
       debug('Adding files to index...')
-      await this.execGit(['add', '.'])
+      await Promise.all(
+        // stagedFileChunks includes staged files that lint-staged originally detected.
+        // Add only these files so any 3rd-party edits to other files won't be included in the commit.
+        this.stagedFileChunks.map(stagedFiles => this.execGit(['add', ...stagedFiles]))
+      )
       debug('Done adding files to index!')
     }
 
diff --git a/lib/runAll.js b/lib/runAll.js
index 1ae43f911..7a4621245 100644
--- a/lib/runAll.js
+++ b/lib/runAll.js
@@ -61,8 +61,8 @@ module.exports = async function runAll(
 
   debugLog('Loaded list of staged files in git:\n%O', files)
 
-  const chunkedFiles = chunkFiles({ files, gitDir, maxArgLength, relative })
-  const chunkCount = chunkedFiles.length
+  const stagedFileChunks = chunkFiles({ files, gitDir, maxArgLength, relative })
+  const chunkCount = stagedFileChunks.length
   if (chunkCount > 1) {
     debugLog(`Chunked staged files into ${chunkCount} part`, chunkCount)
   }
@@ -78,7 +78,7 @@ module.exports = async function runAll(
 
   const listrTasks = []
 
-  for (const [index, files] of chunkedFiles.entries()) {
+  for (const [index, files] of stagedFileChunks.entries()) {
     const chunkTasks = generateTasks({ config, cwd, gitDir, files, relative })
     const chunkListrTasks = chunkTasks.map(task => {
       const subTasks = makeCmdTasks({
@@ -139,7 +139,7 @@ module.exports = async function runAll(
     return 'No tasks to run.'
   }
 
-  const git = new GitWorkflow(gitDir)
+  const git = new GitWorkflow({ gitDir, stagedFileChunks })
 
   const runner = new Listr(
     [