Organic charge transfer (CT) complexes obtained by combining molecular electron donors and acceptors have attracted much interest due to their potential applications in organic opto-electronic devices. In order to work, these systems must have an electronic matching - the highest occupied molecular orbital (HOMO) of the donor must couple with the lowest unoccupied molecular orbital (LUMO) of the acceptor - and a structural matching, so as to allow direct intermolecular CT. Here it is shown that, when molecules are adsorbed on a metal surface, novel molecular organizations driven by surface-mediated CT can appear that have no counterpart in condensed phase non-covalent assemblies of donor and acceptor molecules. By means of scanning tunneling microscopy and spectroscopy it is demonstrated that the electronic and self-assembly properties of an electron acceptor molecule can change dramatically in the presence of an additional molecular species with marked electron donor character, leading to the formation of unprecedented core-shell assemblies. DFT and classical force-field simulations reveal that this is a consequence of charge transfer from the donor to the acceptor molecules mediated by the metallic substrate.