In recent years, graffiti writings are increasingly regarded as a form of art. However, their presence on historic building remains a vandalism and different strategies have been developed to clean or, preferably, protect the surfaces. In this study, an experimental nano-filled coating, based on fluorine resin containing SiO2 nano-particles, and two commercial products have been applied on compact and porous calcareous stones, representative of building materials used in the Mediterranean basin, and their anti-graffiti ability has been analyzed. All the tested experimental and commercial coatings exhibited high hydrophobicity and oleophobicity, thus meeting one of the basic requirements for anti-graffiti systems. The effects of staining by acrylic blu-colored spray paint and felt-tip marker were, then, assessed; the properties of the treated stone surfaces after cleaning by acetone were also investigated. Visual observations, contact angle measurements and color evaluations were performed to this aim. It was found that the protective coatings facilitated the spray paint removal; however high oleophobicity or paint repellence did not guarantee a complete cleaning. The stain from the felt-tip marker was confirmed to be extremely difficult to remove. The cleaning with a neat unconfined solvent promoted the movement of the applied polymers (and likely of the paint, as well) in the porous structure of the stone substrate.