AbstractMicrobial fuel cells (MFCs) made with different types of ceramic membranes were investigated to find a low‐cost alternative to commercially available proton exchange membranes. The MFCs operated with fresh human urine as the fuel. Pyrophyllite and earthenware produced the best performance to reach power densities of 6.93 and 6.85 W m−3, respectively, whereas mullite and alumina achieved power densities of 4.98 and 2.60 W m−3, respectively. The results indicate the dependence of bio‐film growth and activity on the type of ceramic membrane applied. The most favourable conditions were created in earthenware MFCs. The performance of the ceramic membranes was related to their physical and chemical properties determined by environmental scanning electron microscopy and energy dispersive X‐ray spectroscopy. The cost of mullite, earthenware, pyrophyllite and alumina was estimated to be 13.61, 4.14, 387.96 and 177.03 GBP m−2, respectively. The results indicate that earthenware and mullite are good substitutes for commercially available proton exchange membranes, which makes the MFC technology accessible in developing countries.