Fungi play a significant role in the deterioration of various types of monuments. Therefore, the protection of ancient monuments from fungal attacks is an important goal that must attract the attention of researchers worldwide. A total of 69 fungal isolates were recovered from 22 deteriorated objects compromising paper, textiles, wood, and stone in the National Museum of Egyptian Civilization (NMEC) storeroom, Cairo, Egypt. The isolates were identified as 12 different species categorized into three different genera, namely,
Aspergillus
(9 species),
Penicillium
(2 species) and
Trichoderma
(1 species). Among them,
Aspergillus fumigatus
was the most prevalent species. Three essential oils were assessed for antifungal activity and compared with the antifungal effects of five synthetic microcides to identify a natural inhibitory treatment. Thyme oil and sodium azide were found to be the most active growth inhibitors, with minimum inhibitory concentrations (MICs) of 625 and 100 ppm, with inhibition zone diameters of 19.0 ± 0.70 – 23.76 ± 1.15 and 13.30 ± 0.35 – 19.66 ± 0.54 mm, respectively. An in vitro simulation of the biodeterioration process was conducted using spores of the
A. fumigatus
strain NMEC–PSTW.1 on model cubes made of paper, textile, wood, and stone materials. The changes in the characteristics of the artificially deteriorated materials were analyzed using environmental scanning electron microscopy/energy dispersive X-ray spectroscopy and Fourier transform infrared spectroscopy. The results revealed changes in the morphology, physical properties, and chemical composition induced by
A. fumigatus
NMEC–PSTW.1. Overall, thyme oil is recommended as a natural inhibitor to protect carbonate and cellulosic monuments in NMEC against fungal attack.