Yep, I’ve worked with a couple of setups like that, and getting Paychex to push project-level payroll expense detail into QBO isn’t totally straightforward, but it can be done, with caveats.
Out of the box, Paychex doesn’t support native integration that maps expense lines directly to QBO Projects. What we’ve done in the past is build an intermediate step using a custom export from Paychex (you can usually get department/job-level splits if you ask them to turn on the GL mapping by labor codes). From there, we used a third-party tool for data integration to automate the transformation and load it into QBO as journal entries with the correct project tags.
The key is to have a consistent mapping between Paychex job codes and QBO Project names.
