To enhance the spin–orbit interaction in graphene by a proximity effect without compromising the quasi-free-standing dispersion of the Dirac cones means balancing the opposing demands for strong and weak graphene–substrate interaction. So far, only the intercalation of Au under graphene/Ni (1 1 1) has proven successful, which was unexpected since graphene prefers a large separation (∼ $3.3~{\mathring {\rm A}} $) from a Au monolayer in equilibrium. Here, we investigate this system and find the solution in a nanoscale effect. We reveal that the Au largely intercalates as nanoclusters. Our density functional theory calculations show that the graphene is periodically stapled to the Ni substrate, and this attraction presses graphene and Au nanoclusters together. This, in turn, causes a Rashba effect of the giant magnitude observed in experiment. Our findings show that nanopatterning of the substrate can be efficiently used for engineering of spin–orbit effects in graphene.