Silicon oxide barrier layers are deposited on polyethylene terephthalate as permeation barriers for food packaging applications by means of a low pressure microwave plasma. Hexamethyldisiloxane (HMDSO) and oxygen are used as process gases to deposit SiOx coatings via pulsed low pressure plasmas. The layer composition of the coating is investigated by Fourier transform infrared spectroscopy and energy dispersive x-ray spectroscopy to show correlations with barrier properties of the films. The oxygen permeation barrier is determined by the carrier gas method using an electrochemical detector. The transition from low to high barrier films is mapped by the transition from organic SiOxCyHz layers to quartz-like SiO1.7 films containing silanol bound hydrogen. A residual permeation as low as J = 1 ± 0.3 cm3 m−2 day−1 bar−1 is achieved, which is a good value for food packaging applications. Additionally, the activation energy Ep of oxygen permeation is analysed and a strong increase from Ep = 31.5 kJ mol−1 for SiOx CyHz-like coatings to Ep = 53.7 kJ mol−1 for SiO1.7 films is observed by increasing the oxygen dilution of HMDSO:O2 plasma. The reason for the residual permeation of high barrier films is discussed and coating defects are visualized by capacitively coupled atomic oxygen plasma etching of coated substrates. A defect density of 3000 mm−2 is revealed.