In this work the mechanism of (3-aminopropyl)triethoxysilane (APTES) interaction with silicon surfaces is investigated at the molecular level. We studied the influence of experimental parameters such as time, temperature, and concentration on the quality of the APTES layer in terms of chemical properties, morphology, and stability in aqueous medium. This was achieved using a highly sensitive IR mode recently developed, grazing angle attenuated total reflection (GA-ATR). This technique provides structural information on the formed APTES layer. The topography of this layer was investigated by atomic force microscopy in aqueous medium. The hydrophilicity was also studied using contact angle measurement. Combining these techniques enables discussion of the mechanism of silane grafting. Considerable differences were observed depending on the reaction temperature, room temperature or 90 °C. The data suggest the presence of two adsorption sites with different affinities on the oxidized silicon layer. This also allows the optimal parameters to be established to obtain an ordered and stable silane layer. The adsorption of proteins on the APTES layer was achieved and monitored using in situ quartz crystal microbalance with dissipation monitoring and ex situ GA-ATR analyses.