The intercalation of different species in graphene–metal interfaces is widely used to stabilize the artificial phases of different materials, which in some cases leads to the formation of the surface alloys between atoms of the guest metal and the substrate. Here, the interfaces of graphene with Ru(0001) and Ir(111) were modified using intercalation of a thin Mn layer and investigated by means of scanning tunneling microscopy (STM) accompanied by density functional theory (DFT) calculations. It is found that Mn forms a pseudomorphic layer on Ru(0001) under a strongly buckled graphene layer. In the case of Mn intercalation in graphene/Ir(111), a buried thin layer of MnIr alloy is formed beneath the first Ir layer under a flat graphene layer. This unexpected observation is explained on the basis of phase diagram pictures for the Mn–Ru and Mn–Ir systems as well as via comparison of calculated total energies for the respective interfaces.