In this study, a series of sulfonated poly(ether ether ketone) (SPEEK) membranes are prepared and thermally treated in different conditions, i.e., temperature (120-180 degrees C), time (6-42 h), and residual solvent (RS) values (15-45%). Proton conductivity, water uptake, swelling ratio, hydrogen permeability, mechanical properties, and chemical stability of samples are systematically investigated. Also, membranes' characteristics are studied using FTIR, TGA, and AFM. Two stages of "annealing dominated" and "cross-linking dominated" were observed during thermal treatment. Annealing dominated samples exhibited higher flexibility and overall stability with annealing-induced homogenous microstructure while cross-linking dominated samples showed poor mechanical properties and proton conductivity. Results indicate that the treatment of SPEEK membranes with higher RS value facilitates cross-linking at much lower temperatures with a more controlled rate to inhibit excessive cross-linking. Furthermore, response surface methodology suggested that prolonged thermal treatment at low temperatures (<130 degrees C) with RS of around 30% results in sufficient proton conductivity and improved overall stability. (C) 2020 Hydrogen Energy Publications LLC. Published by Elsevier Ltd. All rights reserved.