This study deals with the design of two hydrophobic hybrid SiO₂–TiO₂ materials and their application in the field of monument conservation. The nanocomposite consolidants were based on the modification of tetraethoxysilane (TEOS) with the incorporation of both TiO₂ nanoparticles and hydroxyl-terminated polydimethylsiloxane (PDMS). The TiO₂ nanoparticles have been prepared from the hydrolysis of titanium tetraisopropoxide (TTIP) in the presence of oxalic acid as a catalyst. The physico-chemical properties of the designed hydrophobic nanocrystalline SiO₂–TiO₂–PDMS composites have been extensively studied before their application as consolidants on a limestone. Overall, the effectiveness of the nanocomposites was evaluated by the comparative characterization of untreated and treated stone specimens. The results of both capillary water absorption and contact angle measurements point out that the TiO₂–SiO₂–PDMS nanocomposites functioned as hydrophobic coatings. Furthermore, the results obtained from microdrilling resistance and Fourier Transform Infrared spectroscopy (FTIR) revealed a penetration depth of the nanocomposites within the stone of c. 15 mm. The innovation of these syntheses pertains to the application of hydrophobic semi-transparent and transparent nanocomposites with self-cleaning and strengthening properties, without altering the colour of the stone surface and the water vapour permeability.