My bad, I had forgotten to add my build-system to the list of build-side modules:

(define %foo-build-system-modules
  ;; Build-side modules imported by default.
  `((my-guix build foo-build-system)
    ,@%gnu-build-system-modules))

This fixes it, thanks for you help!

-- 
Pierre Neidhardt
https://ambrevar.xyz/