The Baroque St. Nicholas Church is considered one of the most revered among parishioners, as it has only been closed for three years in its three-century history. The church withstood the German occupation and the battles for the liberation of the city. Its wooden predecessor was of great importance for the state and politics, as it was necessary to put an end to the Time of Troubles and the rumors about the salvation of Tsarevich Dmitry. The church housed many icons of the deceased tsarevich, and he was often commemorated. The church was built at the state’s expense by the order of Mikhail Fyodorovich, who granted significant land holdings to the church. However, the wooden church burned down in 1703, like many other buildings of that time. After Peter I captured Azov, shipbuilding on the Voronezh River declined, and foreign specialists left the city. In the early 18th century, many officials, military personnel, and residents from the Azov territories, which were handed over to the enemy, arrived in the city, and they needed churches. Saint Mitrophan ordered the construction of a new stone church near the site of the burned Dimitrievsky church, the third in Voronezh. In five years, funds were raised and craftsmen were found, and by 1720 the construction was completed. The new church was consecrated in honor of St. Nicholas, Archbishop of Myra in Lycia.

In May 1748, the church survived a severe fire but endured, although it lost much of its interior decoration. The building was repaired, adding an altar in honor of the Great Martyr Demetrius of Thessalonica, and later a bell tower was added. In 1831, Voronezh suffered from a cholera epidemic that claimed the lives of every sixth resident. The epidemic quickly ceased, and the townspeople associated this with the prayers in the Nicholas Church before the icon of the Mother of God of Tolga. After this, the icon was carried through the streets of the city, and believers were healed. In honor of this icon, a new altar was arranged in the church. Since 1881, a church parish charity operated at the church, although the clergy was small: a priest, a deacon, and a psalmist. It is known that before the 1917 revolution, Priest Fyodor Lukin served here. The clergy lived near the church in church houses. Despite their small number, the clergy actively helped during the Russo-Japanese and First World Wars, conducting prayers for the victory of Russian arms and collecting donations for the army and families of the deceased and wounded.

In Soviet times, the chair of the Renovationist bishops of Voronezh was located in the Annunciation Cathedral of the Mitrophan Monastery, and later moved to the Nicholas Church. Parishioners demanded the return of the church to the true Church. Soon, the Bolsheviks became disillusioned with the Renovationist movement, and the church was closed, but not for long. During the Great Patriotic War, the doors of the Nicholas Church were the first among Voronezh churches to reopen for believers in 1942. After the liberation of Voronezh, services resumed and have not ceased since May 1943.