The microporosity, structure and permeability of SiO_x thin films deposited by microwave plasma-enhanced chemical vapour deposition (PE-CVD) and plasma-enhanced atomic layer deposition (PE-ALD) on polydimethylsiloxane (PDMS) substrates were investigated by positron annihilation spectroscopy and complementary technique, such as X-ray photoelectron spectroscopy, infrared spectroscopy, time of flight mass spectroscopy and atomic force microscopy. The SiO_x films were deposited onto spin-coated PDMS substrates, which were previously exposed to an oxygen plasma thus achieving the conversion of the top polymer layer into SiO_x. The presence of this oxidised surface near the region led to an overall decrease in micropore density and to a shift towards smaller pore sizes within the deposited SiO_x films. A correlation between the oxygen fluence during the oxygen plasma treatment and the microporosity of the PE-CVD and PE-ALD SiO_x films could be established.