Fuel cells are at the battlefront to find alternate sources of energy to the highly polluting, economically and environmentally constraining fossil fuels. This work uses an organosilicon molecule presenting two amine functions, bis(3-aminopropyl)-tetramethyldisiloxane (APTMDS) with the aim of preparing cross-linked sulfonated poly(ether ether ketone) (SPEEK) based membranes. The hybrid membranes obtained at varying APTMDS loadings are characterized for their acid, proton conductivity, water uptake, and swelling properties. APTMDS may be considered as an extreme case of silica nanoparticle and is therefore most advantageously distributed within the polymeric matrix. The two amine groups can interact, via electrostatic interactions, with the sulfonic acid groups of SPEEK, resulting in a double anchoring of the molecule. The addition of a small amount of APTMDS is enhancing the mechanical and hydrolytic properties of the membranes and allows some unfolding of the polymer chains, rendering some acid sites accessible to water molecules and thus available for proton transport.