In 1666, a stone church was built in the monastery in honor of St. Nikon of Radonezh, the miracle worker, with an altar dedicated to St. Nicholas. The separately existing wooden church of St. Nicholas was abolished. In 1685, a new separate wooden church was built in honor of St. Nicholas the Miracle Worker, which stood until 1710 when it burned down in a fire in Yuriev. In this same fire, the wooden cathedral church of the monastery, dedicated to the Entry of the Most Holy Theotokos, was also destroyed. The only church that survived the fire was the Nikon church.

In 1725, a stone chapel was added to the Nikon church in honor of the Entry of the Most Holy Theotokos, replacing the burned Entry church. However, from 1763 to 1766, thanks to the efforts of the abbess of the monastery, Agafiya, and the parishioners, a new stone cathedral church was built in honor of the Entry of the Theotokos, featuring five domes. After its construction, the altar of the Entry in the Nikon church was renamed to St. Nicholas.