The alarming increase of pollution has significantly increased buildings maintenance. Nowadays, the economic figures associated to repairing activities are even more relevant than those corresponding to new construction works, especially on heritage buildings. Since the degradation of building materials is the result of a complex combination of physical, chemical and biological agents, the development of multifunctional protective treatments remains a significant challenge. We report a simple strategy to produce a versatile biocidal/superhydrophobic/consolidant treatment by incorporating biocidal Ag nanoparticles (AgNPs) grafted to functionalized SiO2NPs into a silica sol, which can be applied by simple procedures such as spraying. The use of an Ag-SiO2 coupling agent increases biocidal effectiveness up to >90% values due to: (1) an increase of the AgNPs stability; (2) a hierarchical roughness due to the formation of Ag/SiO2NPs clusters; and (3) an enhanced contact with the cell walls. In addition, the synergistic effect allows for an easier removal of the dead cells, increasing the durability of the treatment.