Hydrophobic layers are generated and chemisorbed onto standard coating materials for photovoltaic (PV) devices in order to improve their barrier properties against the atmospheric degradation agents and achieve a higher lifetime for the coated devices. The hydrophobic layers are deposited on PET-–SiOx substrates using two different molecules (alkylsilanes and fluoroalkylsilanes) as precursors. High liquid barrier properties are achieved for the fluoroalkylsilane coated PET-–SiOx, best results being average water contact angle > 130° and average oil contact angle > 90°. A chemical mechanism hypothesis is provided in order to explain the different reactive behavior observed for the PET-–SiOx samples with alkylsilanes and fluoroalkylsilanes, respectively. Moreover, the oxygen barrier properties are significantly improved by the fluoroalkylsilane layer deposited in ethanol, that leads to a 70% reduction of the Oxygen Transmission Rate (OTR) compared to that of the uncoated PET-SiOx substrate.