In this study, we fabricated a bilayer hybrid organic solar cell with P3HT as the donor and ZnO as the acceptor (ITO/ZnO/P3HT/Au). We show that passivating a self-assembled monolayer (SAM) over the ITO electrode surface before fabricating the ZnO layer improves the crystallinity of the ZnO layer and of the P3HT layer spin-coated on top of the ZnO layer. The SAM modification resulted in improved charge mobility in the ZnO and P3HT layers. As a consequence, the short circuit current of the photovoltaic device were enhanced. The power conversion efficiency of the SAM-modified device was approximately 60% higher than that of the untreated device. Our findings suggest that the performance of metal oxide-based organic solar cells can be improved by SAM-assisted modulation of metal oxide crystallinity.