Conservation strategies to limit the degradation of stone materials are being constantly developed. To this aim, new materials are designed to confer hydrophobic properties and anti-graffiti protection to the treated surfaces. Hybrid nanocomposites, based on inorganic nano-particles added to an organic matrix, have been recently proposed for treatments of stone surfaces, obtaining promising and innovative properties. In the present paper, an experimental product based on fluorine resin containing SiO2 nano-particles, a commercial fluorine-based product and a silicon-based material were applied as protective coatings on two calcareous stones (compact and porous) widely employed in the Mediterranean region. All the studied products are expected to provide both water and anti-graffiti protection to both stones’ surfaces. The rheological characterization of the liquid products, changes in color of the surfaces, and variations in water vapor permeability allowed the compatibility of the protective systems applied to stones to be evaluated. Water–stone contact angle measurements and water absorption by capillarity were used to control the action against water ingress. The oleophobicity was assessed by measuring the oil–stone contact angle. The experimental nano-filled product proved to be a suitable hydrophobic coating for compact and porous stones; furthermore, it provides high oleophobicity to the treated surfaces, as required for anti-graffiti systems.