Exploiting single electrical charges and their mutual interactions for computation has been proposed as a concept for future nanoelectronics. Controlling and probing charge transfer in electrically isolated atomic-scale structures are fundamental to push its experimental realization. Here, we controllably inject individual excess electrons and study their distribution in a self-assembled structure supported on a nonconductive substrate. The self-assembly ensures structural order down to the atomic scale. Depending on the charge state of the molecular assembly, intermolecular electron hopping and specific electron distributions have been resolved by atomic force microscopy, clarifying the charge-transfer pathways in the tunnel-coupled structure. 'When mutual charge interactions were exploited, control over specific charge distributions in the self-assembled structure has been achieved with single-molecule precision, paving the way toward the design of data processing platforms based on molecular nanostructures.