In recent years, attention has been paid to finding eco-friendly products that could represent an alternative for the chemicals usually used during conservation procedures. In the field of the devitalization of biological patinas, the most studied products are essential oils (EOs). Several works tested EOs in vitro on microorganisms isolated from stone artifacts but few applied these products on real artworks colonized by a complex patina. In the present work, the biocidal effect of two EOs (cinnamon bark and oregano) and two EO-based products (Biotersus and Essenzio) was compared to that of three chemical biocides commonly used in the conservation of stone artifacts (Biotin R1+R2, NewDes50, and Preventol RI50). The products were applied by brush in situ on a marble slab characterized by a green patina. The biocidal activity was evaluated by analyzing the chlorophyll fluorescence and quantifying ATP through biochemical tests. Furthermore, the products’ interference with stone was evaluated by colorimetric measures on sedimentary rock samples. The results indicate that chemical biocides exhibited biocidal activity of greater than 99.5% with a single application, while cinnamon oil (at a 1% concentration) and Essenzio required two applications to achieve the same level of efficacy. Conversely, oregano oil and Biotersus were not able to effectively reduce microorganism vitality, even with repeated applications.