Multifunctional coatings for the protection and conservation of built cultural heritage are extremely useful for addressing the several and different degradation mechanisms that develop and threaten natural stones, which are exposed to environmental conditions. This study presents the development of a nanocomposite coating, consisting of zinc oxide (ZnO) nanoparticles and a polysiloxane binder, designed to protect limestone heritage by integrating three key properties: extreme water resistance, self-cleaning, and antimicrobial action. According to images obtained by Optical Profilometry, nanoparticles play a crucial role in forming a hierarchical, lotus-inspired structure and increasing surface roughness that imparts enhanced water-repellent properties. Since water is a primary factor in the deterioration of natural limestone, achieving effective water resistance is essential for its preservation. Notably, the wetting properties of the polysiloxane–ZnO composite are comparable with the wettabilities of other composite superhydrophobic coatings, consisting of polysiloxanes and silicon oxide (SiO₂) nanoparticles, which were developed in the past. The polysiloxane selected herein serves two purposes simultaneously: first, it acts as a binder for the nanoparticles, and second, it contributes to the consolidation of the stone. ZnO was selected, instead of other nanoparticles (e.g. SiO₂), because it has photocatalytic and antibacterial properties. The self-cleaning scenario is demonstrated with experiments, which were conducted using methylene blue as a model contaminant. Moreover, it is shown that the suggested coating hinders the incubation of E. coli and S. aureus. Extensive experiments confirm that the designed coating exhibits excellent mechanical, chemical, and thermal stability.