A challenging objective in monumental stone restoration is to synthesize crack-free silica materials for application as consolidants. Hydrophobicity is also a valuable property for such products; it is important to prevent the penetration of water because water is the main vehicle by which the agents of decay enter the pore structure of the stone. We report the development of a hydrophobic crack-free nanomaterial with application to stone restoration. Specifically, organically modified silicate (ormosil) has been synthesized by the co-condensation of tetraethoxysilane (TEOS) and hydroxyl-terminated polydimethylsiloxane (PDMS) in the presence of a nonionic surfactant (n-octylamine). The role played by the surfactant in the assembly of the organic-inorganic hybrid silica gel was investigated. We also prepared a crack-free material using the same synthesis but without adding PDMS to the starting sol. Finally, the effectiveness of the nanomaterials synthesized as a consolidant and hydrophobic protective treatment was evaluated on a particular widely used monumental stone. The high hydrophobicity of the organic-inorganic hybrid product synthesized in our laboratory is discussed as a function of the surface roughness of the material.