We report the size-dependent propagation of gold nanoclusters through few-layer graphene (FLG). We employ aberration-corrected scanning transmission electron microscopy (STEM) to track the fate of Au55 and Au923 clusters that have been deposited, independently and isoenergetically, onto suspended FLG films using cluster beam deposition. We demonstrate that Au55 clusters penetrate through the FLG, whereas the monodisperse Au923 clusters reside at the surface. Our approach offers a route to the controlled incorporation of dopant nanoparticles and the generation of nanoscale defects in graphene.