In 1939 the Communist leader Khorloogiin Choibalsan had the monastery ruined, as part of a purge that obliterated hundreds of monasteries in Mongolia and killed over ten thousand monks. Three small temples and the external wall with the stupas remained; the temples became museums in 1947. They say that this part of the monastery was spared destruction on account of Joseph Stalin's pressure. One researcher claims that Stalin's pressure was connected to the short visit of US vice president Henry A. Wallace's delegation to Mongolia in 1944.
Erdene Zuu was allowed to exist as a museum only; the only functioning monastery in Mongolia was Gandantegchinlen Khiid Monastery in the capital, Ulaanbaatar. However, after the fall of Communism in Mongolia in 1990, the monastery was turned over to the lamas and Erdene Zuu again became a place of worship. Today Erdene Zuu remains an active Buddhist monastery as well as a museum that is open to tourists.
On a hill outside the monastery sits a stone phallus called Kharkhorin Rock. The phallus is said to restrain the sexual impulses of the monks and ensure their good behavior