Morphology can play a critical role in determining function in organic photovoltaic (OPV) systems. Recently molecular acceptors have showed promise to replace fullerene derivatives as acceptor materials in bulk heterojunction solar cells and have achieved >10% efficiencies in single junction devices. The nearly identical mass/electron densities between the donor (polymer) and acceptor (molecule) materials results in poor material contrast compared to fullerene-based OPVs and therefore morphology characterization using techniques that rely on mass/electron density variations poses a challenge. This inhibits a fundamental understanding of the structure–property relationships for non-fullerene acceptor materials. We demonstrate that low angle annular dark field scanning transmission electron microscopy and resonant soft X-ray scattering form a set of complementary tools that can provide quantitative characterization of fullerene as well as non-fullerene based organic photovoltaic systems.