This paper (Part II) aims to provide an understanding of the degradations originating in the membrane or the binder and which dramatically affect the membrane electrode assembly performance and therefore the lifespan of protein exchange memory fuel cells. In Part I, evidence was provided of the corrosion of the platinum catalysts and the diffusion/migration through the membrane of platinum cations. In this paper we establish that these platinum cations induce physical cross-links that modify both the thermomechanical properties and the conductivities of the membrane. Since physical cross-links are reversible, ex situ experiments were performed to recover the performance of pristine membranes by acidic treatment. Membrane performance was found to be much more affected in the case of membranes aged in the hot zone rather than in the cold zone.