Poly-ether-ether-ketone (PEEK) is a high performance polymer with many intrinsic properties. When it is used in the form of coating, an improvement of some of its functional properties was achieved by forming a surface nanolayer. In this chapter, it will be described how it was possible to obtain this result. Firstly, three kinds of PEEK composite coatings were deposited by electrophoretic deposition, adding alumina particles, polytetrafluoroethylene (PTFE) and lignin to PEEK. Then, the composite coatings were thermal treated in a furnace. Therefore, surface nanostructure and chemical composition of these PEEK composite coatings were modified with respect to bulk coatings, due to interaction between PEEK chain and secondary phase, emphasised by the thermal treatment conditions. Experimental evidence of the formation of surface nanolayer was provided by SEM, TEM, GIXRD, ATR-FTIR and XPS characterisations. Functional characterisations demonstrated that wear resistance-in the presence of alumina particles-hydrophobicity-in the presence of PTFE-and corrosion resistance-in the presence of Lignin-were increased with respect to pure PEEK.