The role of the fluoropolymer matrix in the stability of irradiation grafted proton conducting membranes under fuel cell conditions is investigated. The structure of a series of membranes with poly(vinylidene fluoride), poly(vinylidene fluoride-co-hexafluoropropylene), poly(tetrafluoroethylene-co-hexafluoropropylene), and poly(ethylene-alt-tetrafluoroethylene) matrices with poly(styrene sulfonic acid) side chains is studied before and after a fuel cell test using X-ray scattering techniques and confocal micro-Raman spectroscopy. All tested membranes suffer from a loss of poly(styrene sulfonic acid) leading to a decrease in conductivity. Changes in crystallinity, lamellar period, orientation and thickness of the membranes are reported and compared to corresponding properties of the initial polymer films and the pristine membranes. The membranes where most severe changes in the structure of the matrix polymer can be observed have the shortest lifetimes in the fuel cell.