Composites of tin nanoparticles (Sn NP) and graphene are candidate materials for high capacity and mechanically stable negative electrodes in rechargeable Li ion batteries. A uniform dispersion of Sn NP with controlled size is necessary to obtain high electrochemical performance. We show that the nucleation of Sn particles on highly ordered pyrolitic graphite (HOPG) from solution can be controlled by functionalizing the HOPG surface by aryl groups prior to Sn deposition. On the contrary, we observe heterogeneous deposition of micrometer sized Sn islands on HOPG subjected to oxidation prior to deposition in the same conditions. We demonstrate that functional groups act as nucleation sites for Sn NP nucleation, and that homogeneous nucleation of small particles can be achieved by combining surface functionalization with diazonium chemistry and appropriate stabilizers in solution.