An experimental study was carried out for the development and characterization of novel photopolymerizable siloxane-modified methacrylic formulations containing hydroxyapatite (HA) powders for possible use as protective coating for carbonate stone substrates. The experimental formulations were mainly intended for the surface protection of porous stones, in particular those employed in Apuliam monumental, archeological and historical constructions, or wood supports. Amounts of HA particles ranging from 2.5 wt.% to 20 wt.% were added to a siloxane-modified methacrylic mixture, previously investigated. The effect of inclusion of HA particles in the methacrylic mixture on the final properties of the photopolymerizable systems, applied on glass support and on two different carbonate stone elements, was investigated. To this aim, the transparency and scratch hardness characteristics of the coatings, photo-cured on a glass substrate, were firstly measured. Then, the hydrophobic properties and the color change of the same coatings, applied and photo-cured on stone elements, were measured.