The current study reports on the impact of a series of functional alkoxysilanes on the wettability and structure of a well-established silicon/zirconium hybrid anticorrosion sol–gel coating. The selected functional alkoxysilanes comprise tetra ethylorthosilicate (TEOS), 3-glycidyloxypropyltrimethoxysilane (GPTMS), 3-aminopropyltriethoxysilane (APTES) and vinyltriethoxysilane (VTES) and are incorporated at various concentrations (1, 5, 10 and 20%) within the silicon/zirconium sol–gel material. The prepared materials are successfully processed as coatings and cured at different temperatures in the range of 100–150 °C. The characterisation of the structures and surfaces is performed by dynamic light scattering (DLS), scanning electron microscopy (SEM), Fourier transform infrared spectroscopy (FTIR), silicon nuclear magnetic resonance spectroscopy (29Si-NMR), atomic force microscopy (AFM) and static water contact angle (WCA). Structural characterisations (DLS, FTIR,29Si-NMR) show that the functional alkoxysilanes effectively bind at the surface of the reference sol–gel material, resulting in the formation of functional core–shell nanoparticles. WCA results show that the hydrophobic properties of all materials decrease with curing temperature, and AFM analysis demonstrated that this behaviour is associated with a decrease in roughness. The physico-chemical processes taking place are critically assigned and discussed.