Experimental and theoretical studies of manganese deposition on graphene/Ni(111) show that a thin ferromagnetic Ni3Mn layer, which is protected by a graphene overlayer, is formed upon Mn intercalation. The electronic bands of graphene are affected by Ni3Mn interlayer formation through a slight reduction of n-type doping compared to graphene/Ni(111) and a suppression of the interface states characteristic of graphene/Ni(111). Our density functional theory-based theoretical analysis of interface geometric, electronic, and magnetic structure gives strong support to our interpretation of the experimental scanning tunneling microscopy, low energy electron diffraction, and photoemission results and shows that the magnetic properties of graphene on Ni(111) are strongly influenced by Ni3Mn formation.