In this study, we report a systematic investigation of the impact of various processing conditions on all features of the bulk polymer microstructure in working P3HT:PCBM solar cells. Unlike previous studies, which usually examine optimized films grown on Si, without an inorganic electrode layer, we directly examined films in working device architectures to understand the impact of the various steps commonly used in device manufacturing. Thermal treatments were observed to strongly impact the performance of devices produced at less than optimal conditions through changes to the bulk crystal structure; however, even when the production conditions are close to the optimal morphology and crystal structure, annealing is still necessary to improve the π-π overlap of adjacent polymer chains and to reduce the interfacial barrier at polymer-electrode interfaces. The annealing step is therefore crucial to yielding high performance through the control of both the bulk and interfacial properties. Our results suggest a new perspective on device manufacturing, showing that it is not necessary to achieve perfection in bulk crystal structure with the first production steps, potentially saving time in the manufacturing process.