is there any way to set multiple pyproject.toml files in a single repo? We currently have a setup like this and I would like to find a way to get pants working alongside our current build

Yes. Although to better answer that, what are you using these pyproject.toml files for? Poetry requirements? linter config?

we are using them for both right now, but trying to get rid of the first

You certainly can use multiple pyproject.toml files in both contexts. For Poetry, a sort-of gotcha is that Pants creates a single "universe" of your third-party deps, as explained in https://www.pantsbuild.org/v2.8/docs/python-third-party-dependencies . This can cause dependency inference to complain about ambiguity if you have the same project in multiple pyproject.toml files For linter config files, Pants tries to emulate the tools themselves very closely. We automatically find config files for you, using the semantics of that tool, and make sure it's in the chroot. We leave it up to the tool to then do its thing. Some tools complain if >1, some have a subtree override the parent, etc. The net effect is that

./pants lint fmt

should behave the same as when you run directly w/o Pants. Does that make sense?

yeah it does