Hypogean or enclosed monuments are important cultural heritage sites that can suffer biodegradation. Many of the stone walls of the prestigious Domus Aurea are overwhelmed by dense biofilms and so need intervention. Room 93 was chosen as a study site with the aim to test the efficacy of phyto-derivatives as new biocides. Laboratory studies were performed comparing the effects of liquorice leaf extract (Glycyrrhiza glabra L.), lavender essential oil (Lavandula angustifolia Mill.) and a combination of both. In situ studies were also performed to test the effect of liquorice. The results were compared with those of the commonly used synthetic biocide benzalkonium chloride. The effects on the biofilms were assessed by microscopy along with chlorophyll fluorescence analysis. The phototrophs in the biofilms were identified morphologically, while the heterotrophs were identified with culture analysis and 16S gene sequencing. Results showed that the mixed solution liquorice/lavender was the most effective in inhibiting the photosynthetic activities of biofilms in the laboratory tests; while, in situ, the effect of liquorice was particularly encouraging as an efficient and low-invasive biocide. The results demonstrate a high potential biocidal efficacy of the phyto-derivatives, but also highlight the need to develop an efficient application regime.