In the last decade, worldwide research has focused on innovative natural biocides and the development of organic and inorganic nanomaterials for long-lasting reliability. In this work, the biocide effects of two different biocides encapsulated in two different silica nanosystems for a multifunctional coating have been performed through in vitro tests, by using Chlorococcum sp. as a common stone biodeteriogen. Zosteric sodium salt (ZS), a green biocide, was compared with the commercial biocide, 2-mercaptobenzothiazole (MBT), widely used in the treatment of cultural heritage. The analyzed systems are the following: silica nanocapsules (NC) and silica nanoparticles (MNP) not loaded with biocides, two nanosystems loaded with ZS and MBT, and free biocides. The qualitative and quantitative evaluations of biocide efficiency were performed periodically, analyzing pigment autofluorescence to discriminate between active and inactive/dead cells. The analyses showed multiple differences. All the nanocontainers presented an initial reduction in chlorophyll’s autofluorescence. For the free biocide, the results highlighted higher efficiency for MBT than ZS. Finally, the nanosystems loaded with the different biocides highlighted a higher activity for nanocontainers loaded with the commercial biocide than the green product, and better efficiency for MNP in comparison with NC.