The biodeterioration of wooden cultural heritage is a severe problem worldwide and fungi are the main deteriorating agents. The identification of effective natural products, safer for humans and the environment, is a current challenge. Ten deteriorated archaeological objects (a wooden statue of a seated man, an anthropoid wooden coffin with a cartonnage mummy of Nespathettawi, and a wooden box of Padimen’s son), stored at the Egyptian museum in Cairo, were considered here. The wood species of the three most deteriorated objects were previously identified as Acacia nilotica, Ficus sycomorus, and Tamarix gennessarensis. Twenty-six fungal species were isolated and identified from the wooden objects and the four most frequent species belonged to the genus Aspergillus. Fourteen fungal species among those isolated showed the greatest biodeterioration activity on the experimental wood blocks of the archaeological objects. The antifungal activities of several eco-friendly plant essential oils (from cinnamon, eucalyptus, frankincense, geranium, lavender, lemongrass, menthe, rosemary, tea tree, and thyme) and plant extracts (from basil, eucalyptus, henna, melia, and teak) were tested against the fungal species with the greatest biodeterioration activity. The essential oils (Eos) were more effective than the plant extracts. Thyme EO, followed by geranium and cinnamon ones, was the most active (minimum inhibitory concentrations: 0.25–1 µL/mL). These EO; also showed inhibitory effects on the enzymatic activities (cellulase, amylase, and protease) of the four most dominant fungal species. Thymol and p-cymene were the two main components of thyme oil, while geraniol and beta-citronellol were those of geranium oil; eugenol and caryophyllene were those of the cinnamon EO. Thyme oil applied to the most deteriorated experimental aged A. nilotica wooden cubes inoculated with the four highly frequent fungal species was effective in wood preservation. Moreover, no significant interference was observed in the wood before and after thyme treatment. Thyme oil seems to be a promising eco-friendly antifungal agent for the preservation of archaeological wooden artefacts.