Hybrid organic/inorganic solar cells have not lived up to their potential because of poor interface properties. Interfacial molecular layers provide a way of adjusting these devices to improve their performance. We have studied a prototypical system involving poly(3-hexylthiophene) (P3HT) on planar zinc oxide (ZnO) films that have been modified with two types of molecules having identical 18-carbon alkyl chain termination and different surface attachments: octadecanethiol (ODT) and octadecyltriethoxysilane (OTES). We examined the functionalized surfaces using water contact angle measurements, Kelvin probe measurements, infrared absorbance spectroscopy, and atomic force microscopy. These have shown that OTES forms disordered incomplete monolayers, while ODT is prone to develop multilayered islands. Both treatments enhance polymer ordering. However, inverted solar cell devices fabricated with these treated interfaces performed very differently. ODT improves the short circuit current (JSC), open circuit voltage (VOC), and power conversion efficiency (η), while these parameters all decrease in devices constructed from OTES-treated ZnO. The differences in VOC are related to modifications of the surface dipole associated with deposition of the two types of alkyl molecules, while changes in JSC are attributed to a balance between charge transfer blocking caused by the saturated hydrocarbon and the improved hole mobility in the polymer.