Wood is very susceptible to the action of biotic agents. There is a growing interest in the protection of wood and wood artworks to extend their life, using environmentally friendly preservatives. The aim of this paper was the study of nano/siliconate impregnation system for wood protection to control biological colonization. The biotic agents studied have been wood decay fungi. In conclusion, this paper has shown that all the treatments have presented an excellent protective performance against biotic agents. Is important to mention that a synergistic effect can be observed when generating the siliconate/nanoparticle mixtures, resulting in protective systems with excellent efficiency for all the degrading agents. Moreover, it presents an easy application, which represents not only a watertight protective system, but also a set of systems that may be used and managed according to the availability of the active components, the costs, and, most importantly, without having to modify the form of application.