Originally a convent was founded in 1552 on the site of mass graves of Russian soldiers killed during the conquest of Kazan, so that the nuns could pray for their souls. However it was later decided that to prevent it from flooding each spring, it should be moved to Zilantova hill, which gets its name from the legend that Zilant, the winged snake-like monster, once lived here. During the Russian Civil War, the White Army and Czechoslovakian Legion set up defences here, but the city was nevertheless recaptured by the Reds. Upon retaking the city, nine monks were executed by the Reds. These monks are remembered as the Zilantova New-Martyrs. The convent was closed in the 1920s.

By the time it was returned to the Orthodox Church in 1998, virtually nothing was left of the convent's buildings. Reconstruction work started and now all buildings have been rebuilt including the All Saints' Cathedral and the Holy Trinity Cathedral.