It was destroyed on 21 August 2015 by members of the Islamic State of Iraq and the Levant (ISIL or ISIS), whose acts of terror in the Syrian Civil War include widespread vandalism and violence against non-Salafists and historical heritage.

St. Elian Monastery housed a 5th-century tomb and served as a major pilgrimage site, particularly to those seeking a cure for bodily ailments.

[citation needed] Through various excavation efforts throughout the 21st century, the original structure is believed to have been a basic one, consisting of mud and brick walls with simple post and lintel entrances.

Archeologists have also unearthed a large plastered iconostasis and a stone sarcophagus at the site, which some believe contained the bones of Mar Elian himself.

The community led by bp Jacques Mourad rebuilt the monastery, including the crypt and church, and returned the relics of Mar Elian.