Graffiti on facades often has a heavy impact in social and economic terms, particularly when historical and artistic artefacts are affected. To limit the damages to the surfaces, preventive plans are implemented and anti-graffiti coatings are used as a protective measure. In this study, the distribution of a spray paint inside a highly porous stone, with and without anti-graffiti protection, was investigated. Two commercial sacrificial anti-graffiti systems were used and an acrylic-based paint was applied as staining agent. Environmental scanning electron microscopy and energy-dispersive X-ray spectroscopy (EDS) microanalysis were performed to characterise, from the morphological and chemical point of view, the anti-graffiti coatings and the paint. Maps of the main elements were acquired to locate the different products inside the stone. Chemical removers were used to clean the stained surfaces, then the effectiveness of the cleaning was assessed by visual observations and colour measurements, as well as on the basis of percentage of residual stain. The obtained results highlighted that the anti-graffiti efficacy strongly depended on the characteristics of the applied coating. This latter usually acted as a barrier, but good results were obtained only where the stain did not remain as a separate layer, but penetrated the protective coating. Microcracks in the anti-graffiti coating were able to nullify the protective action.