The performance of non‐fullerene, polymer bulk heterojunction (BHJ) organic photovoltaic devices has a significant correlation with the molecular morphology of the donor and acceptor. The authors show that small organic molecules coordinated to a metal oxide, an electron transport seed layer (ETSL), can profoundly modify the donor:acceptor molecular morphology of inverted organic photovoltaic (OPV) devices. Using grazing incidence wide angle X‐ray scattering (GIWAXS), the authors show that a PTB7‐Th:IEICO‐4F BHJ active layer has a higher degree of face‐on molecular alignment on ETSL‐1 (biphenyl‐4,4′‐dicarboxylic acid, coordinated to ZnO), whilst for naphthalene‐2,6‐dicarboxylic acid coordinated to ZnO (ETSL‐2), it is reduced. Devices of PTB7‐Th:IEICO‐4F BHJ prepared on ETSL‐1 had a 19.91% increase in the average power conversion efficiency (PCE), a 1.56% increase in the fill factor (FF), and a 16.66 ± 0.2% enhancement in the short circuit current density. The observed improvements are believed to be due to significant modifications to the oxide‐BHJ interfacial region of ETSL‐1, namely the elimination of nano‐ridges and defect centers, along with an enhanced wettability. These factors can be correlated with the enhanced device performances, leading to the conclusion that the modulation of the molecular morphology of donor:acceptor blends by ETSL‐1 has a broad impact on improving OPV cell efficiencies.