The deterioration of cultural asset is induced by biological, chemical, and physical factors, influenced by anthropogenic activity and environmental conditions. In this study, the contribution of biotechnology is emphasized to define the conservation strategy, for a marble Fountain (Two Dragons, XV century) located in Palermo city center, based on an integrated approach and eco-friendly procedures. Biotechnological protocols are preliminarily applied as an integrated approach, based on microscopy observation, in vitro culture and genomic DNA analysis to recognize and characterize microbial communities. Several biological systems have been identified: green algae (Chlorella) and cyanobacteria (Cyanobium, Oscillatoria); bacteria (Arthrobacter, Bacillus, Micrococcus, Paracoccus); fungi (Alternaria, Aspergillus, Penicillium, Phoma, Fusarium, Cladosporium). In order to address biological colonization, the commercial Tea Tree Oil (Melaleuca alternifolia) and laboratory-distilled (Calamintha nepeta and Allium sativum) EOs, have been assayed by in vitro Agar disc diffusion, Well-plates diffusion, and Micro-dilution methods; the result allows to define the most appropriate EOs concentration to use. In a green conservation prospective, this study highlighted that EOs can potentially replace the traditional biocides, but the activity must be preliminary evaluated by centring the choose specifically on each microbial taxon identified.