Charge-state transitions of a single Cu-phthalocyanine molecule adsorbed on an insulating layer of NaCl on Cu(111) are probed by means of alternate charging scanning tunneling microscopy. Real-space imaging of the electronic transitions reveals the Jahn-Teller distortion occurring upon formation of the first and second anionic charge states. The experimental findings are rationalized by a theoretical many-body model that highlights the crucial role played by the substrate. The latter enhances and stabilizes the intrinsic Jahn-Teller distortion of the negatively charged molecule hosting a degenerate pair of single-particle frontier orbitals. Consequently, two excess electrons are found to occupy, in the ground state, the same localized orbital, despite a larger Coulomb repulsion than the one for the competing delocalized electronic configuration. Control over the charging sequence by varying the applied bias voltage is also predicted.