The monastery was founded around 1567 by Saint German of Kazan as a dependency of the Sviyazhsk Assumption Monastery, which he had led since 1555. The dependency is mentioned in the land survey book of 1565. In 1594, Metropolitan Germogen of Kazan, the future Patriarch of All Russia, asked Tsar Feodor Ioannovich to establish the John the Baptist Monastery in Kazan based on this dependency. On January 28, Feodor Ioannovich issued a decree to open the monastery.

Initially, all buildings were wooden, but in 1649 a fire destroyed them. In 1649 and 1652, the monastery was rebuilt in stone with funds from Moscow merchant Gavriil Fyodorov-Antipin. A unique ensemble appeared in the city center, with all buildings constructed almost simultaneously between 1649 and 1652. Over three years, the magnificent three-cupola John the Baptist Cathedral with two chapels, the five-cupola Introduction Church, and the octagonal bell tower were built. The three-cupola church was initially possibly called the Entry into Jerusalem and was consecrated on September 7, 1652, by Metropolitan Cornelius of Kazan and Sviyazhsk. The church had three differently sized cupolas on octagonal bases supported by a vault. It was adjoined by a refectory with an arched gallery. Of the buildings from that time, the five-cupola Introduction Church and the octagonal bell tower have survived. Unfortunately, the main church, the John the Baptist Cathedral, did not survive. In the 19th century, it was dismantled due to dilapidation and replaced with a new one, which was also demolished in the 1930s. The rest of the ensemble has remained almost unchanged and is a valuable architectural complex in the center of Kazan.

In 1992, the monastery was returned to the Kazan Diocese. The first abbot was David Korablyov, a monk from the Trinity-Sergius Lavra. The reliquary of Saint German with a part of his relics was restored in the monastery. During the construction of the Kazan metro near the monastery and the Nikolsky Cathedral, a pit was dug, which led to cracks in the walls of the Introduction Church. Despite cosmetic repairs, significant damage was inflicted on the architectural monuments.

Since 1994, services have resumed in the restored Introduction Church. The monastery became the second in the Kazan Diocese to be restored after Raifsky. It is known for its charitable activities, including the only free canteen for the needy in Kazan and providing temporary work for the homeless.