Until the mid-17th century, the monastery was surrounded by a wooden fence, with only the Holy Gates and the adjacent northwest wall having stone construction. In the 1640s-1650s, according to a royal decree from 1644, the monks were allowed to make bricks for free, leading to the construction of new brick walls. The construction was completed in 1656, as confirmed by the inscription above the Holy Gates.

The monastery has 5 towers: Belozerskaya at the northern corner, Vologodskaya at the eastern, Southern at the southern, Melnichnaya at the western, and Vodyanaya in the middle of the southwestern wall. They form an irregular polygon resembling a trapezoid, with a total length of 950 meters, featuring towers at the corners and in the middle of the southwestern wall. The northwest wall has an entrance through the Holy Gates with the Ascension Church, where the wall forms an obtuse angle directed outward. The wall thickness exceeds 2 meters, and the height on the southeastern and northeastern sides reaches seven meters. The southwestern wall, facing the Vologda River, is the lowest.

The tall and powerful towers at the northern, eastern, and southern corners of the enclosure protrude significantly beyond the line of the walls and have 16 facets. They were likely designed as the main defensive structures, with several tiers of loopholes for circular defense. The walls between the towers also have loopholes: arched lower ones for close combat, long thin ones in the middle tier, and narrow angled ones in the upper tier for upper combat. Along all walls on the inside, there is a platform for upper combat. In the southeastern and northeastern parts of the enclosure, there were "bags," stone pillars with narrow rooms for storing gunpowder and detaining particularly important criminals. In front of the southwestern wall from the side of the Vologda River, there is an earthen rampart.

The completion of the walls is solid, without separate crenellations. The towers were originally topped with wooden tents with observation towers, replaced in the 18th century with ornate roofs. During the restoration from 1955 to 1960, the Belozerskaya and Vologodskaya towers were covered with shingles, while the others had metal roofs. The facets of the Belozerskaya, Vologodskaya, and Southern towers were painted white, yellow, and orange in the 19th century, while the other towers and walls were whitewashed. Besides the Holy and Vodyanaya Gates, there are Small Gates leading into the monastery through the northeastern wall.

The architectural treatment of the monastery's walls and towers is diverse. The monumental Southern and Vologodskaya towers stand out for their size, about 20 meters, and decorative treatment of the crenellations and machicolations, adorned with polychrome tiles. The Melnichnaya tower has 8 facets and is notable for its decoration, with semi-columns supporting an arcature belt. The Vodyanaya tower is a small quadrilateral, previously a passageway, topped with a wooden tent with a metal covering and has a small guard attic.