Abstract For vacuum web coating for permeation barrier coatings in flexible packaging, the final functionality of the packaging media is extremely dependent on the whole chain of processing steps up to the final laminated packaging film. The most sensitive sector appears to be, on the one hand the hand-shake between substrate film pretreatment–substrate surface properties and the coating process with its characteristics on the other. The influence of different surface pretreatment processes (Corona activation, oxygen and ammonia plasma treatment) on active surface groups of BOPP (biaxial-orientated polypropylene) substrates is shown together with: (1) specifities of the thermal deposition (electron beam source); (2) the reactive deposition–microwave plasma process (plasma species, excitation characteristics, kinetic energies, obtained by in situ process monitoring); and (3) structural properties (chemical composition, adhesion and oxygen permeation) of the thin barrier films (Al 2 O 3 and SiO x ), in correlation with the achieved functional properties of the barrier coated films.