This study examines the magnetic interactions between spatially variable manganese and chromium trimers substituted into a graphene superlattice. Using density functional theory, we calculate the electronic band structure and magnetic populations for the determination of the electronic and magnetic properties of the system. To explore the super-exchange coupling between the transition-metal atoms, we establish the magnetic ground states through a comparison of multiple magnetic and spatial configurations. Through an analysis of the electronic and magnetic properties, we conclude that the presence of transition-metal atoms can induce a distinct magnetic moment in the surrounding carbon atoms as well as produce a Ruderman-Kittel-Kasuya-Yosidalike super-exchange coupling. It is hoped that these simulations can lead to the realization of spintronic applications in graphene through electronic control of the magnetic clusters.