This work focuses on the impact of sulfonated poly(ether ether ketone) (sPEEK) membrane pretreatments on fuel cell performance, starting from two different batches of Fumapem E730 from Fumatech, acquired in 2019 and in 2020. sPEEK membranes are possible lower cost alternatives to perfluorosulfonic acid (PFSA) membranes for proton exchange membrane fuel cells (PEMFC) applications. Before use, they must be pretreated to ensure a complete protonic substitution and removal of residual reagents/solvent: the simplest protocol consists in soaking the membrane in an acid solution followed by a rinsing step in water. In addition to this acidification step, hydrothermal (HT) treatments in water at high temperature for a few hours to a few days were also considered herein, as well as a hydro‐alcoholic (HA) step, because of their expected effects on membrane nanostructure. Overall, four different protocols were used. The membrane water uptake, water self‐diffusion, proton conductivity, and fuel cell performance—under H2/O2—were measured. It was found that in the best case—membranes from the 2020 batch subjected to HA followed by 72 h HT pretreatments—the fuel cell performances exceeded those obtained with a PFSA membrane (Nafion XL). This is explained by a higher protonic conductivity, probably resulting from a better sPEEK nano‐structuration.