The wooden Church of the Presentation was built by Kypriyan between 1212 and 1216, simultaneously with the founding of the monastery. On May 26, 1651, Metropolitan Varlaam of Rostov and Yaroslavl issued a blessing for the construction of a new stone church in honor of the Presentation of the Mother of God at the Mikhailo-Arkhangelsky Monastery. This church was built between 1653 and 1656 with funds from merchant Nikifor Revakin.

The Church of the Presentation, which has one dome, is located on the eastern side of the refectory and was added in 1842, forming a single entity with it. The interior decoration of the church has almost not survived, although it is known that shortly after its construction, a three-tiered gilded iconostasis was installed, which lasted for over a hundred years. In 1765, stoves made of green tiles, crafted by local mason Dmitry Suchkov, appeared in the altar and refectory. The large refectory is particularly impressive, with its western facade adorned with an original triangular pediment featuring an elongated left side and narrow slit-like openings on either side of the central icon case. The layout of the refectory is typical for its time: it consists of a spacious single-column hall for communal meals and adjoining utility rooms to the north, such as the cellar and storeroom. However, the vaulted hall with a massive square pillar in the center, now partitioned, stands out for its large size among other monastic refectories. At the second-floor level, the refectory connects to the main church via a covered passage, accessed by wide stone staircases on both sides.

According to descriptions by Archimandrite Augustine, published in the "Vologda Provincial Gazette" in 1847, to the right in the refectory was a cross carved from white stone and set into a large wooden board. Originally, the cross was located in a wooden chapel built at the site of the death of Prokopyi of Ustyug. In 1737, under Archimandrite Pachomius, the construction of a stone fence began, and the chapel was demolished. In 1814, a stone chapel was built, and the cross was moved first to the Presentation Church and then to the refectory.