The degradation of stone materials is a challenging issue in the cultural heritage field: in particular microorganisms are among the most common agents of stone damage and great efforts have been made to improve the efficacy of antifouling treatments and at the same time to reduce the environmental impact caused by the use of biocides in high concentration. Actually, biocides are applied directly on the surfaces or diluted into coating formulations but because of biocides degradation or to their rapid release and immediate effect such coatings have a quite short-lived antifouling action what could be partly solved by using big amounts of biocides. However, an innovative strategy for controlling the release of bioactive species and reducing their concentration consists in the use of nanocontainers where to introduce the biocides. In order to satisfy ecological requirements and EU regulations in this work two different green biocides, zosteric acid sodium salt and usnic acid, have been selected: zosteric acid sodium salt is a Natural Product Antifoulants (NPAs) derived by Zostera marina (eelgrass), while usnic acid is a lichen secondary metabolites (LSM), well known as potential natural antimicrobial substance. Zosteric acid sodium salt was synthesized while usnic acid is commercially available: they have been tested in SiO2 nanocontainers differing for their morphology. In this work it is reported the preparation and characterization of the empty SiO2 nanocontainers, the one loaded with zosteric acid sodium salt and usnic acid along with their antifouling activity evidencing the possibility to tune the antifouling efficiency by combining the two in different proportions.