The interaction strength of FePc molecules adsorbed on graphene-Co, obtained by intercalation of Colayer(s) under graphene (Gr) grown on Ir(111), has been investigated by core level photoemission and X-ray absorption spectroscopy. Upon intercalation of a single layer of Co beneath Gr, the Co atoms are pseudomorphic with the Ir(111) lattice, inducing a rippled Gr layer with valley and hill regions. FePc molecules, adsorbed on Gr/1 ML Co, are trapped in the valley regions and the Fe metallic centers strongly interact with the Gr/Co system. The intercalation of further Co layers leads to a relaxation of the Co lattice up to the formation of a commensurate (1 x 1) Gr/Co system. The Fe centers of the molecules adsorbed on the flat commensurate Gr/Co are found to be less interacting. We have determined that, even though the organic macrocycles of the FePc molecules, flat lying on the Gr/Co system, are completely decoupled by the presence of the Gr intralayer, the Fe-Co interaction is mediated by the graphene spacer and dependent on Gr corrugation. (C) 2017 Elsevier B.V. All rights reserved.