Broader contextOrganic-based solar cells have the potential of offering a low cost, flexible, light-weight, clean, and quiet alternative energy sources for a variety of applications. The highest efficiency organic solar cell design is the bulk heterojunction (BHJ) architecture (∼5.6%) in which the active layer consists of a blend of electron donating (p-type) and electron accepting (n-type) materials forming an interpenetrating network of the hole and electron accepting components. The interpenetrating network formation depends strongly on the interactions between the donor and the acceptor and processing conditions. Here, we explore the effect of donor–acceptor interactions on the blended film morphology, phase separation, and device characteristics of solution processed diketopyrrolopyrrole-based BHJ solar cells. We found that unlike conjugated polymers, the degree of phase separation before and after thermal annealing of the blends can be controlled by the alkyl substituents on the fullerene acceptor. Changes in film morphology and phase separation lead to significant differences on the performance of the as cast and annealed devices.