Previously, a wooden church dedicated to Nicholas of Zaraysk with an altar of Paraskeva Friday stood on the site of the stone temple, built in 1566. This wooden church burned down in the fire of 1579, which destroyed part of the city near the Kremlin and the entire northeastern part of the settlement.

The stone church in its current form was built in 1728 with funds from merchant Ivan Afanasyevich Miklyaev for the workers of the cloth factory. The main altar was consecrated in honor of the Epiphany of the Lord, the right one in honor of Guriy, Varsanofiy, and German, the Kazan saints, and the left one in honor of Paraskeva Friday. However, the church retained its previous name in honor of the earlier wooden church.

The church served as the center of a small parish that was adjacent to the Kazan Mother of God Monastery. The parishioners were mostly poor, and the monastery provided significant assistance to the church. The church burned several times in city fires until the beginning of the 19th century, and at times only the walls remained.

After the fire of 1815, the church was restored for a long time. The right altar was consecrated in 1821, the main altar was restored in 1831 and renamed in honor of the Nativity of the Most Holy Theotokos. The old Friday altar was dismantled and rebuilt in 1855, probably according to the design of architect F. I. Petondi. The right altar in honor of the three Kazan saints has not survived to this day.

In 1923 and 1937, the church was used as a cathedral for the "renovationists," replacing the Annunciation Cathedral in the Kazan Kremlin. In 1937, the church was closed and turned into a prison for inmates awaiting transfer to camps. Executions were also carried out here, and the executed were buried on the church grounds.

The prison in the Friday church was recalled in the memoirs of the mother of writer V. P. Aksyonov, E. S. Ginzburg. In the 1950s, the bell tower was demolished, and the church fell into disrepair. In the 1980s, cosmetic repairs were made.

In 1993, the church was transferred to the Ministry of Culture of the Republic of Tatarstan, and restoration work began to create an icon museum. In the second half of the 1990s, the church was returned to the Kazan Diocese of the Russian Orthodox Church, and a Chuvash parish was established here. The first benefactors and donors were from the Chuvash diaspora of Kazan and Tatarstan.

In 2000, the bell tower was restored, and in 1999 and 2001, an administrative building was constructed. By the blessing of Archbishop Anastasy Metkin of Kazan and Tatarstan, the iconostasis was painted red in the color of martyrdom. On November 10, 2000, the altar was consecrated in honor of Saint Great Martyr Paraskeva Friday, and on September 21, 2002, the altar in honor of the Nativity of the Theotokos.

In September 2004, a Sunday school was opened at the church, and in September 2010, a parish library began operating. On June 28, 2008, the chapel "All-Merciful" was consecrated, built on the territory of the church complex. It houses the icon of the Mother of God "All-Merciful," which is associated with healing from oncological diseases. The chapel is located opposite the oncology dispensary so that every patient can offer prayers to the Most Holy Theotokos. Daily, a moleben with an akathist for the healing of cancer patients and for the health of all who suffer is served before the icon in the chapel.

Since 2011, the church has been assigned to the Kazan Mother of God Men's Monastery located nearby.