With the present research we describe several alternative approaches aimed at polymer-on-polymer coatings, produced by Plasma Enhanced Chemical Vapour Deposition (PECVD) technique. The depositions were made using two different plasma systems: plasma chamber unit B 30.2 (precursor pentane, hexamethyldisiloxane, perfluorhexane) and PECVD system "Oxford Nanofab Plasmalab System 100" (precursor methane-argon and acetylene-argon). Applying between 3 and 40 min-long cold plasma treatments, in common more than 100 different samples were modified: hydrophobic nanofiltration membranes of type PEEK, as well as ultrafiltration membranes of type PAN and Ultem. Structural and chemical characterisations of the deposited nano-thick functional layers were implemented through SEM imaging, ATR-FTIR, EDX, XPS, AFM and contact angle measurements, which proved the methods' feasibility and properties of the plasma-polymerised coatings. Membrane filtration performance was evaluated by using an 8-position cross-flow filtration system, in terms of permeate flux and rejection characteristics and with styrene oligomers of different molecular weights as markers.