The study explores the application of natural biocides (oregano essential oil and eugenol, directly applied in solutions or encapsulated within silica nanocapsules) for safeguarding stone cultural heritage from biodeterioration, using green algae (Chlorococcum sp.) and cyanobacteria (Leptolyngbya sp.) as common pioneer biodeteriogens. Core-shell nanocontainers were built for a controlled release of microbicidal agents, a safe application of chemicals and a prolonged efficacy. The qualitative and quantitative evaluations of biocide efficiency at different doses were periodically performed in vitro, after six scheduled intervals of time (until 100 days). The release kinetics of composite biocide-embedding silica nanocapsules were characterized by the UV-Vis spectroscopy technique. Data showed both promising potential and some limitations. The comparative tests of different biocidal systems shed light on their variable efficacy against microorganisms, highlighting how encapsulation influences the release dynamics and the overall effectiveness. Both the essential oils showed a potential efficacy in protective antifouling coatings for stone artifacts. Ensuring compatibility with materials, understanding their differences in biocidal activity and their release rates becomes essential in tailoring gel, microemulsion or coating products for direct on-site application.