This study reports on the deposition of nanometre thick siloxane coatings on a poly(ethylene terephthalate) (PET) film using a reel-to-reel atmospheric pressure plasma system. Coatings were deposited in a helium/oxygen plasma, from the siloxane precursors poly(dimethylsiloxane), tetraethylorthosilicate, octamethylcyclotetrasiloxane and hexamethyldisiloxane. Through control of the processing conditions the chemistry of the deposited coatings were tailored to provide a range of hydrophilic (SiOx type) and hydrophobic [SiO(CH3)x] surfaces. The silicon-containing coating surface energies were in the range of 28–70 mN · m−1 and these values were correlated with the surface chemistry. An increase in the hydrophilicity of the coating was found to be associated with a decrease in the concentration of methyl functional groups.