A variety of low-cost hybrid clay based ceramic membranes were developed for application in plant based microbial fuel cells (PMFCs). The membranes were prepared by using locally available clay mixed with varying concentrations of sodium carbonate, sodium metasilicate, boric acid, bentonite, and fly ash. Physiochemical characterization was carried out by using TGA, XRD, FESEM, FTIR, flexural strength test, water uptake, proton conductivity, oxygen and acetate diffusion and compared with Nafion117. Performance of ceramic membranes in PMFCs was evaluated by using the plant E. aureum with carbon fiber brush electrode. Membrane having composition of clay-55%, bentonite-15%, flyash-15%, Na2Co3-8%, Na2Sio3-2%, H3Bo3-5% exhibited maximum power density of 22.38 mW m- 2 which was 78% higher than control (100% clay) with a decrease in internal resistance from 346 omega to 234 omega. The study demonstrates that the addition of bentonite, fly ash, Na2Co3, Na2Sio3 and H3Bo3 with clay at a concentration of 15%, 15%, 8%, 2%, and 5% respectively improved membrane cation transport ability, reducing oxygen diffusion and substrate crossover at the same time. The membrane demonstrated extreme stability for long term operations involving more than six months' period. The low cost of production of clay based ceramic membrane at (sic)1279/ft2 can be a good alternative to highly priced commercially available proton exchange membranes.