The Church of St. Sergius of Radonezh with a refectory was built on the territory of the Ivanovsky Small or Gorniy Monastery, which was part of the Kirillo-Belozersky monastery complex. Initially, the Ivanovsky Monastery was subordinate to the Assumption Monastery, but in the second half of the 16th century, it gained some independence. Some researchers believe that the church was built with funds from Ivan the Terrible and his sons. The first mention of it appears in the monastery inventory of 1601, which states that "in the same Gorniy Monastery there is a stone church with two domes in the name of the venerable Sergius of Radonezh, warm with a refectory."

The year 1560 is considered the year of the church's construction, as it was then that the altar of Dionysius Glushitsky, to whom the chapel is dedicated, was consecrated. The antimension from this altar is kept in the Kirillov Museum. In 1594, the altars of the church and chapel were re-consecrated, associated with the addition of a tier of bells, which was completed with a series of kokoshniks: four on the eastern and western facades and three on the southern and northern. The church was crowned with two domes, one of which was above the temple and the other above the chapel.

From 1621 to 1635, due to the deterioration of the monument, especially the walls of the temple, the bell arches were bricked up, and the belfry was moved to the northern porch added to the refectory and under the eastern wall. In 1997, in honor of the 600th anniversary of the monastery, part of its territory was transferred to the Vologda Diocesan Administration. In 1998, the Orthodox religious organization Kirillo-Belozersky Male Diocesan Monastery was registered.

Today, the churches of John the Baptist and St. Sergius of Radonezh have been transferred to the active monastery. Services in the Church of St. Sergius of Radonezh are held during the summer period.