The Church of John the Baptist with the chapel of St. Cyril of Belozersk was built and consecrated simultaneously with the Church of Archangel Gabriel between 1531 and 1534. It was located outside the monastery walls on a hill, next to a chapel built by St. Cyril of Belozersk. Later, a low stone wall was erected around the church, and this place became known as the Small Ivanovsky Monastery, and the hill itself as Ivanovskaya Hill.

According to the inventory of 1601, the church had "two domes" and a bell tower "on six pillars." The 1668 inventory describes the covering of the church and domes: "The crosses and domes are covered with shingles of white iron." Wooden porches adjoining the western and southern facades are also mentioned. In an icon from 1741 in the collection of the Kirillo-Belozersky Museum-Reserve, the church is depicted with two domes and a four-pitched roof covered with shingles. The 1773 inventory notes wooden staircases at the southern and northern doors, and at the western doors, a stone porch without a vault, sheathed with shingles. It also mentions buttresses at the southeast and southwest corners of the building, "two scaly domes and wooden crosses on the domes covered with tin." This inventory also notes the dilapidated condition of the monument: "the shingle roofs are old," the buttresses "have pulled away from the walls," and there are "cracks in the walls from the vaults to the foundation, and on the southern wall from the foundation up to the vault, large cracks." In the church and altar, there were "eleven windows with old mica window frames in white iron," indicating that by this time, window openings in the niches of the western and southern walls had already been broken through.

Both churches, Gabriel and John the Baptist, were created by the same architect. His good knowledge of contemporary architectural trends indicates that he was not local and most likely came from a major artistic center, possibly from Rostov the Great, as the monastery was under the jurisdiction of the Rostov Diocese at that time.

The Church of John the Baptist did not escape the common fate. The covering over the arches was destroyed, and the small drum was broken. New large windows were cut through in the southern and western walls in place of the niches with paintings. The walls of the church, previously whitewashed, were painted red.

Restoration work on the monument has been minimal. Research allowed S.S. Pod'yapolsky to create a graphic reconstruction of the church, primarily concerning its lost completion. Interior whitewashing was carried out, minimal necessary work for the museification of the monument was done, and the cross that fell from the dome in 1978 was returned to its place.