Git reset --mixed ignores submodules which are not initialized. I've attached a demo script. On one hand, this matches the documentation ("Resets the index but not the working tree"). But on the other hand, it kind of doesn't: "(i.e., the changed files are preserved but not marked for commit)". It's hard to figure out what a mixed reset should do. It would be weird for it to initialize the submodule. Maybe it should just refuse to run? Maybe there should be an option for it to initialize the submodule for you? Maybe it should drop a special-purpose file that git understands to be a submodule change? For instance (and this is insane, but, like, maybe worth considering) it could use extended filesystem attributes, where available. #!/bin/bash mkdir demo cd demo git init main ( git init sub1 && cd sub1 && dd if=/dev/urandom of=f bs=40 count=1 && git add f && git commit -m f ) && ( cd main && git submodule add ../sub1 sub1 && git commit -m 'add submodule' && git tag start ) && # add a commit on sub1 ( cd main/sub1 && echo morx > f && git add f && git commit -m 'a commit' ) && # commit that change on main, deinit the submodule and do a mixed reset ( cd main && git add sub1 && git commit -m 'update sub1' && git submodule deinit sub1 && git reset --mixed HEAD^ && git status # change to sub1 is lost )