Biodeterioration plays a significant role in the damage and loss of monuments including gypsum work. Bacteria and fungi are mainly responsible for the biodeterioration of gypsum work. Thus, the present study aimed to evaluate the effects of essential oils (Thyme, clove, cinnamon, garlic, castor, and olive) on the growth of the main fungi and bacteria which isolated from the Nujoumi Dome which is also called the Dome of the Toshka Martyrs and is located in Aswan, Egypt. Microbial swabs were taken from these infected objects, and the isolated microorganisms were characterized. The next genera were identified: four fungal isolates were isolated and identified as Aspergillus japonicas, Aspergillus terrus, Penicillium commune, and Cladosporium elatum while two species of bacteria were isolated, identified as Bacillus cereus and Listeria monocytogenes. Garlic oil had the best effect on all isolates, showing 35 and 33 mm inhibition of growth of Bacillus cereus and Listeria monocytogenes, respectively, while 28 mm inhabitation of growth of Penicillium commune, 25 mm inhibition of Aspergillus japonicas, and finally 20 mm inhibition of both Aspergillus terrus and Cladosporium elatum. In conclusion, garlic oil could be an effective natural product for controlling the biodeterioration.