The Mongolian revolutionary government removed Tserendorj from his post. He once again took up his duties as chief abbot of Manjushri Monastery and maintained contact with a severely weakened (both physically and politically) Bogd Khan. In 1922 Tserendorj and the Bogd Khan supported a secret mission to contact the Japanese Emperor to request help against the increasing persecution of the Buddhist Church by the new government. In 1930, Tserendorj's personal property was seized as part of the government's rapid implementation of socialist policies. Tserendorj was arrested on charges of anti-government conspiracy and sentenced to 10 years in prison. In 1936
Khorloogiin Choibalsan's Interior Ministry accused him and 24 other lamas of being part of an "anti-revolutionary center". After a show trial that lasted nearly a year, Tserendorj was found guilty and executed in front of the Public Theater in early October 1937.