In this paper, we demonstrate a new way of making low-cost miniature fuel cells for portable applications based on proton conducting porous silicon membranes. Our solution consists in the chemical grafting of silane molecules containing ionizable groups on the pores walls to mimic the structure of ionomer, such as Nafion®, usually used to ensure the proton conductivity of PEM fuel cells. We obtain an inorganic, dimensionally stable, proton conducting membrane with many optimizable parameters such as the pore size, the pore structure of the membrane and the nature of the grafted molecules. Moreover, the use of a silicon substrate offers advantages of serial and parallel integration, the possibility of encapsulation by wafer bonding and gas feed and electrical contacts can be included into the membrane etching process thanks to simple KOH wet etching processes and metal sputtering. A power density of 17mWcm−2 was obtained.