Fullerene-based acceptors have dominated organic solar cells for almost two decades. It is only within the last few years that alternative acceptors rival their dominance, introducing much more flexibility in the optoelectronic properties of these material blends. However, a fundamental physical understanding of the processes that drive charge separation at organic heterojunctions is still missing, but urgently needed to direct further material improvements. Here a combined experimental and theoretical approach is used to understand the intimate mechanisms by which molecular structure contributes to exciton dissociation, charge separation, and charge recombination at the donor–acceptor (D–A) interface. Model systems comprised of polythiophene-based donor and rylene diimide-based acceptor polymers are used and a detailed density functional theory (DFT) investigation is performed. The results point to the roles that geometric deformations and direct-contact intermolecular polarization play in establishing a driving force (energy gradient) for the optoelectronic processes taking place at the interface. A substantial impact for this driving force is found to stem from polymer deformations at the interface, a finding that can clearly lead to new design approaches in the development of the next generation of conjugated polymers and small molecules.