The objective of this work was to isolate and identify fungal strains colonizing painted limestone rectangular funerary Stela of Dedusobek (Cairo CG 20236 \ Sr 3-9714)–Egyptian Museum, and evaluate the resistance effects of isolated fungi to essentials oils nanoemulsion (cinnamon, tea tree, and lemon). Essential oils (EOs) have been well-known for their antimicrobial properties and EOs have also been applied to treat the biodeterioration of cultural heritages as powerful source in green conservation. The use of essentials oils nanoemulsion as an alternative to traditional biocides should be considered. In the present study, we used the tea, lemon, and cinnamon oil nanoemulsions as antimicrobial agents to treat Stela-born fungal deterioration. Our study showed that cinnamon oil nanoemulsion had strong antimicrobial activity in vitro assays, which has been successfully confirmed by application on the biofilm revealed in the painted limestone Stela. The applied essentials oil nanoemulsion were characterized using scanning electron microscopy (SEM) as well as color measurements by CIELAB system. The results revealed that the antimicrobial activity of cinnamon oil nanoemulsion solution was enough to kill the fungal contaminants.