In the late 17th century, a magnificent bell tower was built on the site of the old belfry, preserving some elements of the foundation, which has survived to this day. It has five tiers and is designed in the form of an "octagon on a square," characteristic of architecture from the mid to late 17th century.

The upper part of the bell tower was created based on the model of the bell tower of the Moscow High-Petrov Monastery. However, the craftsmen did not fully copy the existing model: they turned the octagon so that its edge faced the plane of the square. In the 17th century, a trend emerged in Russian architecture towards rich decoration of buildings, both externally and internally. The monastery bell tower built during this period looks festive: in three bands of the octagon and in the middle tier of the square, tiles with bas-reliefs of seraphim and various fruits are installed in the recesses.

This work belongs to the Belarusian master Stepan Ivanov, known as Stepan Polubes. The corners of the bell tower are adorned with half-columns, and windows of various sizes with arched lintels are framed with beautiful brick moldings. Each window has its practical purpose: to illuminate the stairway to the bell tower, the porch, the sacristy, and utility rooms.

The height of the building from the base to the top of the cross is about 55 meters. Previously, a wide staircase led from the lower tier to the warm church, refectory, and porch. The second tier housed the sacristy and library. The third square tier was equipped with battle clocks with special bells for the hours.

Currently, the clock mechanism is stored in a museum in Kolomenskoye, where one of the surviving bells from this bell tower is also located. The clocks operated on the principle of modern timepieces: two heavy weights descended in a shaft that passed through all three lower tiers. Today, the clock face has survived, and an electronic mechanism marks every quarter-hour with a melodic chime and every hour with the ringing of the bell. The upper two tiers were intended for ringing, with the bells located in the lower octagonal tier. To amplify the sound, earthenware hollow vessels were embedded in the vaults and walls.

A description from 1859 mentions nine bells. In 1932, by the order of Comrade Baranov, the bells were thrown down, including a bell cast 11 years after the death of St. Pafnutiy. To this day, one bell has survived, which is now an exhibit at the Kolomenskoye Museum. In 1992, the Russian-American company "LTD Kodi" gifted the monastery 16 new bells, cast in Moscow. On the largest of them, weighing 750 kg, it is inscribed: "The bell was cast by the charity of Paskotinov Vladimir Kondratievich and the family of Jerry Radny, Cherry, Kodi, Lynn Jerry for the Nativity of the Mother of God of the Pafnutiev Borovsky Monastery. By the blessing of Archbishop of Kaluga and Borovsk Clement." With the revival of monastic life in the monastery, the restoration of the refectory and bell tower began. First, the foundations were strengthened, and the buttresses erected 100 years ago against the western wall of the refectory were dismantled as unnecessary.

In the renovated premises of the bell tower's basement, the Museum of Russian Icons was established, opened and consecrated by Metropolitan Clement of Kaluga and Borovsk in 2012. Above the entrance to one of the museum's rooms, a unique 16th-century fresco painting, the Savior Not Made by Hands, has been preserved.