In the field of stone protection, the introduction of inorganic nanoparticles, such as TiO2, ZnO, and Ag in polymeric blends can enhance the protective action of pristine treatments, as well as confer additional properties (photocatalytic, antifouling, and antibacterial). In the framework of the “Nano-Cathedral” European project, nanostructured photocatalytic protective treatments were formulated by using different TiO2 nanoparticles, solvents, and silane/siloxane systems in the blends. The results about the characterization and application of two promising nano-TiO2 based products applied on Apuan marble and Ajarte limestone are here reported, aiming at investigating the complex system “treatment/stone-substrate”. The nanocomposites show better performances when compared to a commercial reference siloxane based protective treatment, resulting in different performances once applied on different carbonatic substrates, with very low and high open porosity, confirming the necessity of correlating precisely the characteristics of the stone material to those of the protective formulations. In particular, the TiO2 photocatalytic behavior is strictly linked to the amount of available nanoparticles and to the active surface area. The alkyl silane oligomers of the water-based formulation have a good penetration into the microstructure of Ajarte limestone, whereas the solvent-based and small size monomeric formulation shows better results for Apuan marble, granting a good coverage of the pores. The encouraging results obtained so far in lab will be confirmed by monitoring tests aiming at assessing the effectiveness of the treatments applied in pilot sites of historical Gothic Cathedrals.