The temple, known as "Nikola the Wonderworker of Gostin", is mentioned in the census books as early as 1565. It was located in the trading square at the Gostiny Dvor and was consecrated in honor of the patron saint of merchants, Saint Nicholas the Wonderworker. Although the exact date of the stone church's construction is unknown, its architecture indicates the 16th century.

According to the census books, the church "Nikola the Wonderworker of Gostin" was situated behind the fish row, and its construction was the merit of priest Grigory and the laypeople. Priest Grigory, deacon Pyotr Isakov's son, and poor elders who received food from the church lived in the churchyard. The state salary included four rubles and bread, as well as church income from wax, incense, and wine. The sexton was entitled to half a kopeck and grain. In the alley behind the Gostiny Dvor, there were yards on both sides.

The future Patriarch of Moscow and all Russia, Germogen, served as a priest in this church and played an important role in the acquisition of the miraculous Kazan Icon of the Mother of God in 1579.

In 1594, Metropolitan Germogen of Kazan and Astrakhan wrote about the apparitions and miracles of the Kazan Icon of the Mother of God, recalling how, while being a priest at Saint Nikola Gostiny, he was moved to tears before the image of the Mother of God and received the archbishop's blessing to take the icon.

In the early 17th century, an altar dedicated to the Kazan Icon of the Mother of God was added to the church, and in 1634, a cold Transfiguration church was built nearby.

Today, the building of the former Nikolo-Gostinodvorskaya Church has lost both of its spires and has partially sunk underground. Until 2017, it housed archival services, including the apparatus of the Main Archive Administration under the Cabinet of Ministers of the Republic of Tatarstan and the State Committee of the Republic of Tatarstan for Archival Affairs.

On August 30, 2017, the "Foundation for the Revival of the Church of Nikola Gostinodvorskaya" was registered, established by the Kazan Diocese of the Russian Orthodox Church.