Sulfinated-sulfonated PEEK was synthesized via partial reduction of sulfochlorinated PEEK with aqueous Na2SO3. From these polymers, covalent-ionically cross-linked ionomer blend membranes were prepared by mixing the sulfinated-sulfonated PEEK with different base-modified polysulfones (PSU-base), followed by cross-linking with 1,4-diiodobutane. These membranes have been compared with covalently cross-linked membranes which were obtained by the cross-linking of sulfinated-sulfonated PEEK and with ionically cross-linked membranes obtained by mixing sulfonated PEEK with different PSU bases. The membranes have been characterized in terms of thermal stability by means of thermogravimetry (TGA) and coupled TGA-FTIR, in terms of cross-linking extent by extraction experiments, in terms of proton conductivity by impedance spectroscopy, and finally, in terms of water uptake by gravimetric analysis.