The effect of microbial activity on the deterioration of archaeological stone items is a worldwide issue, and conserving them with low-toxicity, ecologically benign and naturally biocides is a difficult undertaking. Molecular identification of the microbial communities from a deteriorated archaeological object (Ptahshepses stone statue) located from the Saqqara excavation, Giza, Egypt was recorded. Six essential oils (EOs) (black cumin, clove, geranium, lavender, lemongrass, and thyme) were tested for antimicrobial activity against six degrading fungal and bacterial species. Alternaria alternate, Aspergillus flavus, A. niger, Cladosporium halotolerans, Penicillium crustosum, and Trichoderma viride and three bacterial species, Pseudomonas protegens, P. putida, and Serratia odorifera, were isolated. Of the most effective EOs, thyme showed the highest inhibition percentage (143.4%) against Serratia odorifera, followed by P. putida (135%), and Pseudomonas protegens (131.5%). Lemongrass and clove EOs had minimum inhibitory concentrations (MICs) ranging from 0.5 µL/mL to 2 µL/mL for all isolated deteriorated fungal and bacterial species, while the lowest efficiency EOs were lavender, geranium and black cumin. It can be concluded that thyme and lemongrass EOs have a potential use for protecting the Ptahshepses stone statue from microbial deterioration.