The first church dedicated to St. Nicholas the Wonderworker was built on the site of the future monastery in 1675. Later, in 1685, a new Nicholas church was consecrated, becoming the second in the monastery. According to a description from 1732, the church was low, had a transept on the north side, a refectory, and a porch. It had a four-pitched roof without a dome, and the cross was covered with white iron. The royal doors in the church were painted. Unlike the Trinity church, the Nicholas temple was heated in winter, but it was dismantled in 1763 due to dilapidation.

In 1797, a new wooden church in honor of the apostles Peter and Paul was built on the site of the Nicholas church. In 1875, the roof was covered with iron. According to I. Tokmakov, by the end of the 19th century, the church preserved a five-tiered iconostasis from the 17th century with images brought during the foundation of the monastery. In 1893, restoration was completed: a stone foundation was laid, two lower crowns were replaced, and the porch and gallery were rebuilt. The church was heated, but it burned down on December 31, 1897.

From 1900 to 1904, a stone church in honor of St. Nicholas the Wonderworker was built on the site of the burned Peter-Paul church, consecrated in June 1905. With the altar, the length of the church was 33 meters. The architecture of the Nicholas church combined elements characteristic of the time of construction and an earlier period. The church had five domes, with minimal vertical and horizontal divisions on the walls. The facades were adorned with a curved wooden cornice, often found in urban residential buildings. An important part of the architecture was the monumental framing of the doorways on the southern and northern facades.

By the beginning of the monastery's revival, the extensions above the main cornice were removed, and the building had a regular roof. By 2012, the church regained its bulbous five-domed shape.