Among the fuel cell technologies, the polymer electrolyte membrane fuel cells (PEMFCs) are particularly promising because they are energy-efficient, clean, and fuel-flexible (i.e., can use hydrogen or methanol). The great majority of PEM fuel cells rely on a polymer electrolyte from the family of perfluorosulfonic acid membranes, nevertheless alternative materials are currently being developed, mainly to offer the alternative workout techniques which are required for the portable energy sources. Plasma polymerization represents a good solution, as it offers the possibility to deposit thin layer with an accurate and homogeneous thickness, even on 3D surfaces. In this paper, we present the results for the growth of proton conductive fluoro carboxylic membranes elaborated by plasma enhanced chemical vapour deposition. These membranes present conductivity values of the same order than the one of Nafion®. The properties of the membrane, such as the chemical composition, the ionic conductivity, the swelling behaviour and the permeability were correlated to the plasma process parameters. The membranes were integrated in fuel cells on porous substrates and we present here the results regarding the barrier effect and the power output. Barrier effect similar to those of 40μm Nafion® layers was reached for 10μm thick carboxylic membranes. Power outputs around 3mWcm−2 were measured. We discuss the results regarding the gas barrier effect and the power outputs.