Recently, an intermixed phase has been identified within organic photovoltaic (OPV) bulk heterojunction (BHJ) systems that can exist in addition to relatively phase-pure regions, highlighting the need for a refined picture of the solid-state microstructure of donor–acceptor blends and for gaining further understanding of the exact nature and role such intermixed phases play in such devices. Here we manipulate the microstructure of polymer–fullerene systems via processing means and the selection of the molecular weight of the donor polymer. This manipulation is used as a tool to vary the fraction of intermixed phase present and its effects on the structure and subsequently the opto-electronic processes. We find clear relationships between the state of mixing and amount of exciton quenching and number of polarons generated per absorbed photon. Furthermore, we observe that blend systems incorporating higher molecular weight polymer result in a greater yield of dissociated polarons, likely due to the increase of the intermixed fraction.