We compare the structures of the theory of causal fermion systems (CFS), an approach to unify Quantum Theory with General Relativity, with those of modified measure theories (MMT), which are a set of modified gravity theories. Spacetimes with MMT can be obtained as the continuum limit of a CFS. This suggests that MMT could serve as effective descriptions of modifications to General Relativity implied by CFS. The goal is to lay the foundation for future research on exploring which MMTs are consistent with the causal action principle of CFS.