Abstract In this study a conservation treatment of stone monuments meant for consolidation, protection, and inhibition of biofilm formation is proposed. The method is developed as a part of a systematic investigation aimed at producing nanocomposite coatings able to exert a marked biological activity over a long period of time thanks to their peculiar structure. Zinc oxide nanoparticles, synthesised by means of simple and reproducible electrochemical procedures, are embedded in commercially available and commonly used consolidant/water repellent matrices to obtain nanostructured materials. Products based on tetraethoxysilane and/or polysiloxanes were tested. In a first step the nanomaterials were applied on stone samples and studied with scanning electron microscopy and spectrophotocolorimetry. Then, in situ experimentation was undertaken by applying nanocomposite coatings on the exterior of a 12th-century church in the south of Italy. The performances of the ZnO-nanoparticles based composite coating were compared with a previously investigated copper nanoparticles based material, successfully tested and monitored in situ for more than two years. Finally, preliminary tests on the inhibitory effect on the growth of the fungus Aspergillus niger were also carried out. The results showed that in case of zinc oxide a tenfold higher concentration of nanoparticles as compared with Cu-NPs can be utilized in the matrices without affecting the colour of the stone substrate, which means that the new material should be able to exert a long-lasting biocide activity. Laboratory and in situ tests of the developed innovative nanomaterials yielded very promising, though preliminary, results in terms of chromatic changes, morphological characteristics and bioactivity. Constant monitoring of the coatings will be continued in order to obtain all necessary information on their long term behaviour and inhibition of biological colonisation.