After Git 2.38 (specifically after commit 6061601d9), git no longer honors safe.directory settings in files that are [include]'d from the main global configuration file, even though they are shown as being in global scope by `git config --show-scope --show-origin`. The docs added by https://github.com/git/git/commit/779ea9303a7de3d618f3b0e329ebb89529ab3285 only talk about scopes and do not mention anything about [include] being specifically ignored. $ git config --get-all --show-scope --show-origin safe.directory global file:/home/grawity/.config/git/config /srv/this.works global file:/home/grawity/.config/git/config.local /srv/this.does.not.work # ~/.config/git/config (owned by grawity:users) [safe] directory = /srv/this.works [include] path = ~/.config/git/config.local # ~/.config/git/config.local (also owned by grawity:users) [safe] directory = /srv/this.does.not.work -- Mantas Mikulėnas