diff --git a/lib/gitWorkflow.js b/lib/gitWorkflow.js
index f7dea4f64..ecc6502bc 100644
--- a/lib/gitWorkflow.js
+++ b/lib/gitWorkflow.js
@@ -68,14 +68,16 @@ class GitWorkflow {
       debug('Done backing up merge state!')
     }
 
-    // Save stash of entire original state, including unstaged and untracked changes.
-    // This should remove all changes from the index.
-    // The `--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)
+    // Get stash of entire original state, including unstaged changes
     await this.execGit(['stash', 'save', '--quiet', '--include-untracked', STASH])
-    // Apply only the staged changes back to index
+    // Apply index from previous stash back to enable running tasks against
+    // staged files only. `git stash --keep-index` cannot be used here because of
+    // a bug affecting deleted files. The bug has been fixed in git v2.23.0
+    // See https://github.com/git/git/blob/master/Documentation/RelNotes/2.23.0.txt#L322
     await this.execGit(['stash', 'apply', '--index', await this.getBackupStash()])
-    // Checkout everything just in case there are unstaged files left behind.
+    // Clear any unstaged changes since they are saved in the stash,
+    // and shouldn't be affected by tasks
+    await this.execGit(['clean', '-df'])
     await this.execGit(['checkout', '.'])
     // Since only staged files are now present, get a diff of unstaged changes
     // by comparing current index against original stash, but in reverse