The bell tower must have existed by the time of the consecration of the cathedral, but the first wooden hipped belfry of St. Sophia Cathedral was mentioned only in 1622, "some carpenters were hired... and a wooden belfry of eight walls was being built". In addition to 11 bells it had a quite rare in those days in Russia curiosity - a clock. The fire, which destroyed or damaged structures of the Archbishop's house in 1636, did not spare the bell tower either, and instead a temporary structure was put up: "the pillars were set up".

In 1641 a new belfry was built, a few more bells were hoisted on it and a new clock was installed- "chimes striking quarters" - which had a "face" and struck quarters of an hour. In 1653, Archbishop Markel in his petition to the Russian tsar gave the following description of the state of this structure: "and the wooden bell tower, Sir, is dilapidated, and logs of the walls are going out", and asked for permission to use the stones, stored up for the unfinished fortress of Ivan the Terrible, to build a new stone belfry.

After the tsar’s approval the first stone bell tower was erected in 1654-1659. A high eight-faced pillar with pilaster-strips and an open upper tier of the belfry was capped with a slender tent with a small cupola. And of the "Kirillov monastery elder Michael repaired the chiming clock, ...and made the clock face and connected chimes to the bells". The great bell, the evangelist, beat each hour, and six smaller bells - quarters of an hour. In 1698, the bell tower damaged by a lightning strike, the burnt roof and cupola were soon restored. But for about twenty years it was not possible to fix the tent: a lot of Vologda artisans were mobilized for construction sites and shipyards by Peter the Great, and besides there was lack of funds. Since then, ministers have repeatedly stated that "from the sound of the bells bricks are falling down and therefore there’s danger of big collapse".

In 1868, in preparation for the celebration of the 300th anniversary of St. Sophia Cathedral Bishop Paul decided to heighten the belfry, which, in  the opinion of its contemporaries "did not conform to the dignity of other buildings". The provincial architect A. I. Ivanitsky worked out a measurement drawing of the old bell tower and at least two projects of its reconstruction (one of them, "in ancient taste", where the belfry resembles Moscow Ivan the Great Bell Tower, is known). In 1869-1870 the same A. I. Ivanitsky (but not his successor at a position at that moment V.N. Shildkneht as previously believed) implemented the project of reconstruction of the Belfry in pseudo-Gothic style. Though in the composition and certain details of the structure architectural trends of Ancient Russia can be seen. The upper part of the bell tower (the tent and the pillars of the bell tier) were dismantled, and on the basis (pillar) strengthened by buttresses a new upper part was overbuilt, which was higher than the former one by 15 fathoms (32 meters).

With the money of the citizens V.A. Zasetskaya and A. P. Nabalova new chimes were purchased in Moscow in the firm «Butenop Brothers », and then installed in 1871.

In 1967 the stopped because of worn parts mechanism was restored by the Vologda museum watchmaker V.A. Korol’kov and the foreman of mechanics of the plant «Severny Kommunar» B. N. Sosin. Since 1968, every ten years the main mechanism of the clock is fully disassembled, some of its details are washed and polished.

The main mechanism of the Vologda chimes consists of three winding mechanisms: one - for running the clock hands (running), another - for the striking of the clock, and the third one – for beating quarters of an hour.

The mechanisms are in a closed room in the center of the bell tower, between the belfry tier and the observation deck. In the heart of the clock mechanism there is the Graham course, consisting of an escape wheel with 30 teeth and an anchor, connected to a pendulum with the help of a fork. At the ends of the anchor curved inside cylindrical pallets are fixed with plates and screws – an entry plaque and an exit plaque. The chassis weight is 8 poods. To the right of the chassis there is a mechanism of quarters which beats every 15 minutes in a special way. It is driven with the 9-pood weight. When the last quarter is beaten, the leverage goes to the clock striking mechanism on the left of the chassis. The chimes are produced with the help of the 12 - pood weight, connected to the striking mechanism and the hour bell. From the escape wheel a shaft goes upwards, which has a transfer on four shafts going to dial mechanisms. The chimes are winded by hand every three days with a margin of 8 hours.

In 1701, when according to the decree of Emperor Peter I bells all over Russia were being documented to withdraw the fourth part of «bell copper» on military needs, the Cathedral's bell tower had 22 bells weighing 1039 poods 5 pounds in total. The fourth part of the weight of St Sofia’s bells was 259 p. 31 f. with a quarter, but none of the bells of the bell tower was taken down. In February 1701, 2 broken bells weighing 46 poods 3 pounds, 181 poods 26 pounds of red caldron copper and 32 poods 2 pounds and a quarter of pure English rod tin on 22 carts were sent to Moscow Cannon Yard. "And over that quarter 200 poods of red caldron copper are sent for addition." And in March 1702, following the star’s deed with a «gracious word» two bells were delivered to Vologda: one weighing 176 pood 20 pounds, the other - 23 poods 6 pounds.

The bigger of those bells is known today as Big Swan, it was cast by a famous master Ivan Motorin – the creator of the Tsar Bell. So zeal of Archbishop Gabriel contributed to the decoration rather than destruction of the Vologda cathedral bell tower.

A number of bells have names: Big (aka Festive, cast in 1687 in Lubeck, weighing 462 poods 23 pounds), Archangel (aka Jubilee, cast in 1869 in Kadnikov District of Vologda province by master S. D. Chatyshnikov weighing 302 poods 29 pounds), Big Swan (cast in 1691/92 by master I.F.Motorin, weighing 176 poods 20 pounds), Small Swan (cast in 1756 in Vologda district by master M. A. Kolokolnikov, weighing 100 poods), Clock (cast in 1627 in Amsterdam), Vozdvyzhensky (aka Vsednevnyy, cast in 1739 in Vologda District by master I. K. Sokharev, weighing 223 poods).

As an example, we will present the published by N. I. Fedyshin (and earlier with gaps – by N. A. Suvorov) inscriptions on the Big Bell. At the top of the bell a chronicle (an inscription with ligature) is cast in two lines : «In the 7194th year of the World Creation (or in 1686 Anno Domini) on the 20^th of May, at power of pious tsars and grand princes Ioann Alexeyevich, Petr Alexeyevich of whole Russia, blessed by reverend Gabriel Archbishop of Vologda and Beloozersk, in the second year of his blessed flock, this bell was cast for Vologda house of God’s Word of Wisdom, for Catholic and Apostolic Church, for the glory of God the Father. Amen. Weight of 400 poods in it". At the lower edge of the bell there is an inscription in Latin with the date of its casting: «Albert Benninck me fecit Lubecae. Anno 1687" ("Albert Benninck made me in Lübeck in the year of 1687"). The discrepancy in the dates of inscriptions is explained by the fact that the inscription with ligature was made of wax in Vologda and sent to the master to install into the mold. But for some reason, Albert Benninck delayed the implementation of the order until 1687, the year which he indicated in his inscription.

St. Sophia Cathedral was closed on March 18, 1924, as well as the Resurrection Cathedral on March 5, 1938. Between these events, on December 16, 1929 after passing the Decree of the Presidium of the Central Executive Committee "On Regulation of Bell Ringing in Churches" and the Resolution of the Presidium of the Vologda City Council on December 29, 1929 the bells in all Vologda churches were prohibited. On January 30, 1930 there followed the Decree of the Presidium of the Vologda city Council on removing the bells of all Vologda churches.

On February 9, 1930 at 11:00 am at St. Sophia Cathedral a meeting was held by members of the Union of militant atheists. After that, the participants were divided into groups that headed to the prescribed places of work, and the bells were removed from 12 belfries of the town. However, they were not allowed to throw the bells from the cathedral belfry, which was transferred to the museum.

Since the summer of 1988 magnificent festive ringing of the cathedral belfry has returned into the cultural life of Vologda, having become its indispensable attribute. Every Sunday at midday, a concert rehearsal of the bell music band is conducted.