The first wooden belfry of St. Sophia Cathedral was built at the end of the 16th century but burned down during the Polish-Swedish intervention on September 22, 1612. A new wooden belfry was constructed in the 1620s. According to the land survey book of 1627, it had an octagonal shape with a tented top covered in "scales" and was equipped with two tiers, three staircases, a clock, and eleven bells. This belfry also burned down in 1636, and in its place, another wooden one was erected in 1642.

In 1654 and 1659, the wooden belfry was replaced with a stone one. It was an octagonal structure with a stone tented top and a small dome. The stone was taken from Ivan the Terrible's Kremlin. In 1863, the belfry had 14 bells and a clock. The previous belfry can be judged by the preserved belfry of the Vladimir churches, built in its likeness.

In the 1860s, under Bishop Palladius of Vologda, the tented top and bells of the belfry were removed. In 1869 and 1870, on the preserved lower tier, about 17 meters high, a taller belfry was built in the pseudo-Gothic style, designed by architect V. N. Shildknecht. Its height now reaches 78.5 meters, making it the tallest in the Vologda diocese. The upper tier of the belfry features an observation deck, topped with a gilded dome and cross.

The belfry houses bells made by Dutch, Russian, and German masters from the 17th, 18th, and 19th centuries. Among the 17th-century bells, notable ones include the "Clock", "Great Lent", "Water Carrier", "Small Swan", adorned with "herbs", chronicle vines, and stamps depicting saints from the abolished Nikolayevsky Ozyorsky Monastery of 1656, the "Large" or "Festive" bell weighing about 7580 kg, cast in Lübeck in 1687, the "Large Swan", and the "Archangel". The "Large Swan" bell was cast by I. F. Motorin, the creator of the famous Tsar Bell.

In 1701, there were 22 bells in the belfry. In December 1871, new clocks with four chimes were installed on the belfry. When bells were being described across Russia in 1701 for the extraction of a quarter of "bell metal" for military needs, two broken bells, a lot of copper of various grades, and tin were sent to Moscow instead of the Sophia bells. In gratitude from Peter I, the Vologda residents received a charter, and in 1702, two bells as a gift, one of which was Motorin's "Large Swan". In total, the new belfry had 26 bells, all of which, except for the smallest one, have survived to this day. The bells of St. Sophia Cathedral were once again put to use starting in 1989.