The important role of processing conditions, phase separation, and device geometry on open circuit voltage, Voc, is examined for regioregular poly(3-alkylthiophene) (P3AT) solar cells with hexyl, octyl, dodecyl, and hexadecyl solubilizing side chains. Both bilayer and bulk heterojunction devices were investigated. In bilayer devices with C60 as the electron acceptor, thermal annealing produces large increases in Voc for short side chain P3ATs, concurrent with a suppression of the dark forward current and associated reduction in the saturation current density, J0. Systematic measurements of J0 versus temperature revealed clear Arrhenius behavior and a significant decrease in the exponential prefactor for J0 for the annealed devices, while there was very little change in the activation energy barrier (φ) for annealed versus unannealed cells. In bulk heterojunctions based on P3ATs and [6,6]-phenyl-C61-butyric acid methyl ester (PCBM), correlated changes in J0 and Voc were dominated by dependence of the P3AT highest occupied molecular orbital (HOMO) position on both the side chain length and the degree of mixing with PCBM, which was manipulated by employing solvent annealing to drive phase separation. Overall, the device data and analysis presented here demonstrate that, in both the bilayer and bulk heterojunction solar cells, the impact of side chain length on J0 and Voc is dependent on phase separation morphology, which can be manipulated by choice of device architecture and processing conditions.