Thin films, containing fluorocarbons and sulphonic acid groups, were prepared by plasma polymerisation of 1,3‐butadiene/CF3SO3H and styrene/CF3SO3H mixtures using two different types of plasma discharges. The morphology, density, and chemical composition of the synthesised plasma polymers were examined by SEM, small‐angle X‐ray reflectometry, and FTIR and XPS analyses, respectively. Proton conductivity was measured with electrochemical impedance spectroscopy. The prepared films are relatively uniform and free from defects. Plasma materials exhibiting higher sulphonic acid group contents and lower densities are those formed, from the styrene/CF3SO3H mixture, in the after glow discharge configuration; which proves that the kind of discharge and the nature of the monomer mixture have a large influence on the microstructure of plasma materials. Consequently, plasma films, prepared in the after glow discharge from the styrene/CF3SO3H mixture, show proton conductivities (up to 9.8 × 10–2 mS cm–1) about one order of magnitude higher than films prepared in the glow discharge (up to 2.2 × 10–3 mS cm–1 and 2.5 × 10–3 mS cm–1 for films prepared from 1,3‐butadiene/CF3SO3H and styrene/CF3SO3H mixtures, respectively). When compared to the commercially available Nafion®, the reference electrolyte polymer in the PEMFC, our most competitive plasma polymers are intrinsically 100 times less conductive. Nevertheless, due to their thinness (about 1 μm), these plasma films show specific resistances (about 1.0 Ω cm2), which are lower than that of the Nafion® membrane (1.9 Ω cm2 specific resistance). This explains their potential significance as polymer electrolyte membranes in a miniaturised PEMFC.