The main objective of this research is to determine the optimal application conditions of a newly synthesized multifunctional coating containing Ag-doped TiO2 nanoparticles when used as a possible protective agent for sandstone. Firstly, Ag-TiO2 nanoparticles with anatase structure, spherical shape and controllable sizes were prepared using the sol–gel method and characterized. The biocidal activity of Ag-doped TiO2 NPs was studied by comparing its performance to pure TiO2 NPs against two representative Gram-positive and Gram-negative bacterial strains, under both visible irradiation and in the dark; then, the antimicrobial efficiency of two different concentrations of Ag-TiO2 nanoparticles (0.1–1 mol%) was evaluated against two phototrophic strains commonly isolated from deteriorated surfaces. Results showed that the photoactivation and photokilling activity of TiO2 were highly improved by doping with Ag. Next, prepared nanopowders were dispersed in a binder with different powder/PDMS ratios: (0.1, 0.2, 0.5 and 1% w/v TiO2) and then applied in different amounts (2, 3 and 6 g/m2) on Serena stone specimens. Results revealed that the application of 2 g/m2 nanocomposite at powder/binder ratios equal to 1% w/v TiO2 provided a fine hydrophobic character for the stone material with acceptable chromatic variations.