The exchange of virtual photons between quantum optical emitters in cavity QED or quantum nanophotonic setups induces interactions between them which can be harnessed for quantum information and simulation purposes. So far, these interactions have been mostly characterized for two-level emitters, which restrict their application to engineering quantum gates among qubits or simulating spin-1/2 quantum many-body models. Here, we show how to harness multi-level emitters with several optical transitions to engineer a wide class of photon-mediated interactions between effective spin-1 systems. We characterize their performance through analytical and numerical techniques, and provide specific implementations based on the atomic level structure of Alkali atoms. Our results expand the quantum simulation toolbox available in such cavity QED and quantum nanophotonic setups, and open up new ways of engineering entangling gates among qutrits.