A plasma discharge process has been developed that allows the growth of biosensor gate oxides with adapted surface properties for the direct application of biomolecular immobilization cascades. The process involves an accurate selection of processing conditions, mainly, low temperature evaporation of (3-aminopropyl)triethoxysilane (APTS) and dynamic power and flow conditions. Room temperature evaporation of APTS was achieved by designing a vessel with an internal capillary network. The initial high power (100 W) plasma conditions were replaced by milder molecular fragmentation (50 W, 25 W) in a pure Ar discharge. Under these conditions the thin SiO(2) layers presented graded properties with a denser layer at the Si (100) interface and a hybrid organic-inorganic structure at the surface. The chemistry of the films was analysed by Fourier transformed infrared spectroscopy (FTIR) and Rutherford backscattering spectroscopy combined with elastic recoil detection analysis (RBS, ERDA), which confirmed the presence of the SiO(2) and organic phases. Contact angle measurements indicate the higher contribution of the basic polar component to the surface free energy. Furthermore, the higher affinity of the surface towards biomolecular immobilization was confirmed by fluorescence microscopy. Finally, penetration of nitrobenzaldehyde was obtained by application of a molecular permeation method evaluated by UV-vis spectroscopy onto fused silica substrates.