In this study, a preventive method for fighting bio-deterioration of stone substrates is proposed. This is based on the use of bioactive zinc oxide nanoparticles (ZnO-NPs), which are able to exert a marked biological activity over a long period of time due to their peculiar structure. ZnO-NPs are synthesised by a simple and reproducible electrochemical procedure. The nanomaterials are embedded in consolidant/water-repellent matrices to obtain nanostructured coatings. Commonly used products based on tetraethoxysilane and/or polysiloxanes were tested. The resulting nanomaterials were fully characterised by X-ray photoelectron spectroscopy (XPS) to investigate the amount and composition of the NPs and the behaviour of the nanocomposites. Inductively coupled plasma mass spectrometry (ICP-MS) was used for the study of the release of metal from the composites when put in contact with artificial rainwater. The nanocomposites were applied to specimens composed of three different types of stone and chromatic changes upon curing were measured by spectrophotocolorimetry. Finally, morphological characterization by scanning electron microscopy (SEM) was performed. The bioactivity of ZnO-NPs nanocomposites was also assessed in preliminary tests against Aspergillus niger fungus.