The influence of manganese atom intercalation on the electronic structure of graphene grown on Au/Co(0001)/W(110) and SiC(0001) substrates is experimentally studied by angle-resolved photoelectron spectroscopy. Dispersion dependences of the graphene π states at the K point of the Brillouin zone are obtained for both systems using ultraviolet photoelectron spectroscopy, and these dependences exhibit shifts of the Dirac cone induced by manganese intercalation followed by annealing. The structure of the near-surface layers of the systems is investigated by X-ray photoelectron spectroscopy. An analysis of the core level lines indicates the possibility of formation of a thin Mn2Au layer on the graphene–Mn–Au interface and a quasi-two-dimensional Mn layer under graphene on the SiC substrate. A comprehensive Raman spectroscopy study of graphene on SiC demonstrates that the buffer layer remains coupled to the substrate and does not transform into an additional graphene layer after the Mn intercalation of this system. After intercalation, the amount of lattice defects in graphene increases.