Looks like regression in 2.16. Worked fine before update. Seems like git stash is not always working. Any ideas? $ git --version git version 2.16.0.windows.2 $ git config pull.rebase true $ git config rebase.autoStash true $ git status On branch develop Your branch is behind 'origin/develop' by 3 commits, and can be fast-forwarded. (use "git pull" to update your local branch) Changes not staged for commit: (use "git add <file>..." to update what will be committed) (use "git checkout -- <file>..." to discard changes in working directory) modified: source_work/xxxxx.cpp no changes added to commit (use "git add" and/or "git commit -a") $ git pull Created autostash: 7ddcdf2ba HEAD is now at ba14a4c3f some commit Cannot rebase: You have unstaged changes. Please commit or stash them. $ git status On branch develop Your branch is behind 'origin/develop' by 3 commits, and can be fast-forwarded. (use "git pull" to update your local branch) You are currently rebasing. (all conflicts fixed: run "git rebase --continue") Changes not staged for commit: (use "git add <file>..." to update what will be committed) (use "git checkout -- <file>..." to discard changes in working directory) modified: source_work/xxxxx.cpp no changes added to commit (use "git add" and/or "git commit -a") $ git rebase --abort Applied autostash. $ git stash Saved working directory and index state WIP on develop: ba14a4c3f some commit $ git status On branch develop Your branch is behind 'origin/develop' by 3 commits, and can be fast-forwarded. (use "git pull" to update your local branch) Changes not staged for commit: (use "git add <file>..." to update what will be committed) (use "git checkout -- <file>..." to discard changes in working directory) modified: source_work/xxxxx.cpp no changes added to commit (use "git add" and/or "git commit -a") $ git stash Saved working directory and index state WIP on develop: ba14a4c3f some commit $ git status On branch develop Your branch is behind 'origin/develop' by 3 commits, and can be fast-forwarded. (use "git pull" to update your local branch) nothing to commit, working tree clean -- Sincerely, Dimitriy Ryazantcev