Microbial colonization can lead to various biodeterioration phenomena in outdoor stone monuments. To prevent these issues and mitigate the negative effects of chemical control, recent research has focused on encapsulating biocides in nanostructures. We tested the antifouling efficiency of the new multifunctional coating through in situ experiments performed on the Aurelian Walls in Rome. We selected two different biocides (2-mercaptobenzothiazole and zosteric sodium salt) and loaded them into two different silica nanocontainers (nanocapsules and mesoporous particles), which were dispersed in TEOS coatings. These coatings were applied to four common lithotypes (marble, travertine, mortar, and brick). Subsequently, we accelerated the colonization by inoculating microorganisms onto half of the samples, subjecting all samples to aging cycles. We conducted colorimetric, infrared spectroscopy, and other microscopic analyses to assess their durability and antimicrobial action. Our 3-year survey indicates that the coatings demonstrated antifoulant efficiency across all samples, with higher effectiveness observed on brick and mortar compared to travertine and marble. Among the nanostructures, nanocapsules exhibited greater efficiency than mesoporous particles, and regarding the biocides, the commercial one outperformed the natural one. These findings highlighted the potential of such systems in preserving cultural heritage; however, further research and product development is imperative for practical implementation.