The proton exchange membrane (PEM) is a key element of a polymer electrolyte fuel cell, and radiation-grafting is an attractive option for the synthesis of PEMs. Via a systematic investigation of a well-defined model material, sulfonated polystyrene grafted poly(ethylene-alt-tetrafluoroethylene), ETFE-g-PS(SA), we show that the performance and stability of radiation-grafted PEMs in fuel cells strongly depends on the microstructure of the underlying base polymer. The nanoscale structure of the base polymers, grafted films, and membranes is probed by small-angle scattering, and the nanoscale proton dynamics is probed by quasi-elastic neutron scattering. The results of these techniques correlated with fuel cell relevant properties including proton conductivity and water uptake and fuel cell performance clearly indicate that differences in the arrangement of the crystalline phase in the otherwise chemically identical semicrystalline base films can have considerable impact, representing an essential aspect to consider in the development of proton exchange membranes prepared via preirradiation grafting.