Chemical doping offers promise as a means of tailoring the electrical characteristics of organic molecular compounds. However, unlike for inorganic semiconductors used in electronics applications, controlling the influence of dopants in molecular complexes is complicated by the presence of multiple doping sites, electron acceptor levels, and intramolecular correlation effects. Here we use scanning tunnelling microscopy to analyse the position of individual Li dopants within Cu- and Ni-phthalocyanine molecules in contact with a metal substrate, and probe the charge transfer process with unprecedented spatial resolution. We show that individual phthalocyanine molecules can host at least three distinct stable doping sites and up to six dopant atoms, and that the ligand and metal orbitals can be selectively charged by modifying the configuration of the Li complexes. Li manipulation reveals that charge transfer is determined solely by dopants embedded in the molecules, whereas the magnitude of the conductance gap is sensitive to the molecule-dopant separation. As a result of the strong spin-charge correlation in confined molecular orbitals, alkali atoms provide an effective way for tuning the molecular spin without resorting to magnetic dopants. © 2013 Macmillan Publishers Limited. All rights reserved.