> # Trying again with submodule.recurse > git config --global submodule.recurse true > git clone main clone4 cd clone4 > git checkout with-submodule > # Submodule is still not automatically updated (sub folder is empty) > # It seems like submodule.recurse does not affect git clone That is true; submodule.recurse is not affecting git clone. This was a design decision once it was introduced, as the git clone might be too large. Maybe we need to revisit that decision and just clone the submodules if submodule.recurse is set. The problem that this bug report highlights, is the following: Each branch has its own .gitmodules file and they can be all different, however at clone time we only clone submodules from the currently active branch. So you could get your test case to pass with git clone --branch with-submodule main clone5