A complete PECVD process for the plasma polymerization of miniature proton exchange membranes (PEM) is presented. Styrene and trifluoromethane sulfonic acid are used as plasmagen precursors in a capacitive coupled low pressure discharge. The process is monitored by impedance probe measurements to ensure stability and reproducibility. FTIR analyses show that such membranes are mainly made up of a polystyrene-like matrix with grafted sulfonic acid groups, which proportion is tuneable as a function of the plasma parameters. The best results in term of deposition rate, monomer structure retention and PEM performances are obtained under pulsed plasma conditions, enhancing radical processes compared to continuous plasma. Because of their thinness and cross-linked structure, such membranes exhibit a similar proton conduction ability and a methanol permeability reduced by a factor 150 compared to Nafion$^{\circledR}$. SEM observations show a good compatibility of plasma polymerized membranes whatever the substrate is. Consequently, PECVD process enables their better integration in micro fuel cells compared to conventional spin coating method.