In organic solar cells (OSCs), the energy of the charge-transfer (CT) complexes at the donor-acceptor interface, E , determines the maximum open-circuit voltage (V ). The coexistence of phases with different degrees of order in the donor or the acceptor, as in blends of semi-crystalline donors and fullerenes in bulk heterojunction layers, influences the distribution of CT states and the V enormously. Yet, the question of how structural heterogeneities alter CT states and the V is seldom addressed systematically. In this work, we combine experimental measurements of vacuum-deposited rubrene/C bilayer OSCs, with varying microstructure and texture, with density functional theory calculations to determine how relative molecular orientations and extents of structural order influence E and V . We find that varying the microstructure of rubrene gives rise to CT bands with varying energies. The CT band that originates from crystalline rubrene lies up to ≈0.4 eV lower in energy compared to the one that arises from amorphous rubrene. These low-lying CT states contribute strongly to V losses and result mainly from hole delocalization in aggregated rubrene. This work points to the importance of realizing interfacial structural control that prevents the formation of low E configurations and maximizes V .