The monastery was damaged in 1688 during one of the many wars between Dzungars and Khalkh Mongols.
Abtai Sain Kan, mongolski vladar Khalkhov in dedek Zanabazarja, prvi Jebtsundamba Khutuktu, je odredil gradnjo samostana Erdene Zuu leta 1585 po srečanju s 3. dalajlamo in sprejetjem tibetanskega budizma kot državne religije Mongolije.