Nafion membranes were shown to be suitable substrates for atomic layer deposition (ALD) process. ALD utilising trimethyl aluminum as a precursor leads to well reproducible formation of smooth single-sided Al2O3 coating on the membranes. Physicochemical and mechanical properties of the coated membranes were compared to those of the unmodified ones. The coating reduced water uptake and thus also conductivity. Moreover, the Al2O3 coating decreased the oxygen permeability of the membrane by 10 % and the methanol permeability 30-50 %. The mechanical properties of the Nafion® membrane were improved. The resulting membranes were successfully applied in hydrogen fuel cells, direct methanol fuel cells and microbial fuel cells. In the microbial fuel cell, the Al2O3 coated membrane showed stable performance during long-term measurements of more than 100 d and doubled power densities in comparison to a cell equipped with a pristine membrane. The membrane modification strategy has potential for improving the performance of various types of membrane fuel cells and could be used for several types of functional membranes containing active groups for ALD growth.