Using density functional theory (DFT) calculations and angle-resolved photoemission spectroscopy (ARPES) the structural and electronic properties of graphene on the surface and subsurface Co–Ir alloy are investigated upon the intercalation of Co in graphene/Ir(111). It is found computationally that the interaction strength between graphene and substrate is strongly affected by the composition and nature of an alloy, implying the large difference in the electronic structure of monolayer graphene on CoxIr1−x/Ir(111) and Ir/CoxIr1−x/Ir(111). Our theoretical results are supported by ARPES data, which demonstrate the disappearance of the Dirac cone when graphene lies on Co and its restoration upon the formation of the subsurface Co–Ir alloy.