On July 8, 1579, nine-year-old Matrona found an icon at a place indicated to her in a dream. Priest Ermolai, who later became Patriarch Germogen and was recognized by the Church as a martyr, was the first to record the story of this event and the first miracles from the icon. The discovery of the icon just 27 years after Kazan was taken by Russian troops became a symbolic event for contemporaries. That same year, by the decree of Ivan IV the Terrible, a women's Bogoroditsky monastery was founded at the site of the finding. According to tradition, the first nun was Matrona herself, who received the name Mavra after her tonsure.

In 1612, the militia of Minin and Pozharsky took the Kazan icon on a campaign to Moscow with the blessing of the Kazan Metropolitan Ephraim. After their return, the icon was placed back in the Bogoroditsky Monastery of Kazan, which became a well-known shrine of the Middle Volga due to the influx of pilgrims.

By Catherine II's reform, the monastery was classified as second class, and in 1809, as first class. The number of nuns and novices increased from over 100 in the early 19th century to 500 by the time of the revolution. After the closure of Kazan Kremlin in 1918, the main surviving relics of the Kazan diocese were transferred to the monastery. Although the monastery was abolished, an Orthodox community operated here in the 1920s. In 1931, it was moved to the Peter and Paul Cathedral, after which most of the monastery was destroyed.

From 1942, a tobacco factory was located on the territory of the former monastery, and the western part was built up with houses. The Church of the Exaltation of the Holy Cross housed the philological faculty of Kazan Pedagogical Institute. In 1994, the Sofia Church was returned to the believers, and in 2004 and 2005, the Church of the Exaltation of the Holy Cross. On July 21, 2005, Patriarch Alexy II handed over to the Kazan diocese the Vatican list of the Kazan Icon of the Mother of God, which was placed in the church and became a pilgrimage site.

Since 2005, the monastery has been revived as a men's monastery, although it was previously women's. The brotherhood consists of several members. The tobacco factory was removed from the monastery's territory, and during excavations, the remains of nuns were found and reburied in the monastery necropolis on October 12, 2019.

On November 4, 2015, the President of Tatarstan, Rustam Minnikhanov, signed a decree to create the Bulgarian Islamic Academy and to recreate the Cathedral of the Kazan Icon of the Mother of God. The decree provided for events to lay commemorative stones in May and July 2016, as well as the establishment of memorial signs in honor of those who contributed to these projects. Participants of the II Forum of the Orthodox Community of Tatarstan supported the decree and called on everyone to assist in the revival of the shrine.

On April 27, 2016, archaeological excavations began at the site of the former cathedral. On July 21, 2016, Patriarch Kirill consecrated the site for the foundation of the restored Cathedral of the Kazan Icon of the Mother of God.