By using grazing incidence x-ray diffraction and scanning tunneling microscopy experiments, we determine the interface structure of a C 60 layer deposited on a Co(0001) surface. The room temperature deposition gives rise to a (4 × 4) molecular structure with a 10% vertical relaxation of the underneath Co atoms. When annealed around 550 K, the interface undergoes a structural change with most of the buckyballs sitting in a seven Co vacancies nanohole. Ab initio calculations show that this interface reconstruction is stabilized by a strong C-Co hybridization and has a significant impact both on the interfacial magnetic anisotropy that is decreased and on the molecular spin polarization that it increased.