It is impossible to run git commands affecting a different repo from within a `git rebase --exec` because in that environment the `GIT_DIR` and `GIT_WORK_TREE` variables are set and inherited by any commands run as part of `git rebase --exec`. A minimal reproduction is shown below: git init touch file git add file git commit -m"Commit" git rebase --root --exec="git clone . subrepo" It is a bit convoluted for the sake of being self contained. But any git command in `--exec` acting on a different repo than the one being rebased will fail. See my ticket on CMake [0] for a more real usecase. As mentioned in the other ticket, unsetting these variables will work around the issue. git rebase --root --exec="env -u GIT_DIR -u GIT_WORK_TREE git clone . subrepo" [0] https://gitlab.kitware.com/cmake/cmake/issues/18778 Regards