Thin film and bulk, sulfonated poly(ether ether ketone) (SPEEK) have been subjected to a thermal treatment at 160–250 °C for up to 15 h. Exposing the films to 160 °C already causes partial desulfonation, and heating to temperatures exceeding 200 °C results in increased conjugation in the material, most likely via a slight cross‐linking by H‐substitution. It is well‐known that the sulfonate proton plays a major role in the desulfonation reactions, and exchanging the protons with other cations can inhibit both protodesulfonation as well as electrophilic cross‐linking reactions of the sulfonate group with other chains. Yet, the implications of such ion‐exchange for the thermal processing of sulfonated polymer films has not been recognized. Our study demonstrates that the ion exchange stabilizes thin films and bulk SPEEK up to temperatures exceeding 200 °C, opening up ways for the thermal processing of SPEEK in the temperature range of 160–220 °C without adverse effects.