The conservation of stone monuments is a constant concern due to their continuous weathering, in which biofouling plays a relevant role. To enhance the effectiveness of biocidal treatments and to avoid environmental issues related to their possible toxicity, this research aims at formulating and characterizing a coating charged with an eco-friendly biocide and showing hydrophobic properties. For this purpose, zosteric sodium salt—a natural biocide product—has been encapsulated into two silica nanocontainers and dispersed into a tetraethoxysilane-based (TEOS) coating also containing TiO₂ nanoparticles. The coatings were applied on four different types of stone: brick, mortar, travertine, and Carrara marble. The effectiveness of the coating formulations and their compatibility concerning the properties of coated stones were assessed. The results showed that all coatings conferred a hydrophobic character to the substrate, as demonstrated by the increase of the static contact angle and the reduction in the capillary water absorption coefficient. The transmission of water vapor of the natural stones was preserved as well as their natural aspect. Furthermore, the coatings were homogeneously distributed on the surface and crack-free. Therefore, the protective capability of the coatings was successfully demonstrated.