The method consists of the formation of a layer over a stone substrate to increase its hardness, chemical resistance, wear and scratch resistance, comprising applying on the substrate a coating matrix incorporating an organic material and fillers including inorganic nanoparticles and/or microparticles; chemically binding said matrix to the substrate, by a self-assembly process and/or a binding process by covalent bonding, electrostatic bonding, van der Waals bonding or hydrogen bonds; and finally drying said matrix. The mentioned organic material is selected from organosilanes, organophosphates, polycarboxylic compounds, compounds based on triazine heterocycles and said nanoparticles are nanoparticles of oxides, carbides, borides, nitrides of metals or of semimetals.