Biodegradation is among the most common issues affecting Cultural Heritage stone materials in outdoor environments. In recent years, the application of chemical agents with biocidal activity has been the most usual practice when dealing with biofilm removal. In outdoor environments, the use of these biocides is not effective enough, since the materials are constantly exposed to environmental agents and atmospheric pollutants. Thus, it becomes necessary to protect the surface of Cultural Heritage works with antimicrobial coatings to either prevent or at least limit future colonization. In this study, innovative biocides—both natural and synthetic—were applied on a Roman mosaic located in the Archaeological Park of Ostia Antica to compare their effectiveness in removing the biological degradation affecting it. In addition, an antimicrobial coating called “SI-QUAT” was applied and analyzed in situ. SI-QUAT has recently entered the market for its prevention activity against biocolonization. The biocidal activity of these products was tested and monitored using different analytical portable instruments, such as the multispectral system, the spectrocolorimeter, and the bioluminometer. The analyses showed that promising results can be obtained using the combination of the biocide and the protective effect of Preventol® RI50 and SI-QUAT.