The modern bell tower, built in 1603 near the previous bell tower above the cellar cells, was constructed with funds from D.I. Godunov. It is modeled after the cathedral bell tower in Rostov the Great, but smaller, in the form of a gallery with three arches. Under the two lower arches are storerooms, while under the upper one, in four vaulted spans, are the bells. Above the northern span, which looks like a quadrangular tower and rises above the other parts of the building, is a tall tent-like stone top, later enlarged and covered with sheet metal. In this tower, parts of the mechanism of ancient chime clocks have been preserved, which likely belong to the type of clocks on the Novgorod Euphemia Tower. According to an inscription on the chime bell, these clocks were installed in 1659 with funds from D.I. Godunov. On the western side, a stone terrace with an iron roof has been added to the bell tower, accessed by a stone staircase with iron railings.

In 1908, the bell tower was renovated, and the exterior painting on the tent tower was updated on three sides. However, due to the rapid deterioration of the painting and its inconsistency with the decoration of the Trinity Cathedral, it was decided in 1912 during the restoration of the Ipatiev Monastery to return the bell tower to its original appearance. The monastery's bell tower currently houses 10 bells. Among the old ones, the largest bell weighing 600 poods was cast on September 20, 1648, by order of Tsar Alexei Mikhailovich. This bell was likely recast from a previous bell, also weighing 600 poods, which was donated to the monastery by the mother of Boris Godunov. The second largest bell originally weighed 172 poods and was cast during the reign of Tsar Boris Godunov. After a crack, it was recast in 1894, increasing its weight to 208 poods 2 pounds. The third bell, weighing 104 poods 25 pounds, was recast in 1812. The fourth bell, weighing 68 poods, was gifted by D.I. Godunov and recast on August 1, 1659. The fifth and sixth bells were recast during the reign of Tsar Alexei Mikhailovich. The origins of the remaining bells are not dated. In 1912, the tent top of the bell tower was covered with green tiles, and some windows and arches were opened to restore the bell tower's former appearance.

The historical set of bells on the bell tower of the Holy Trinity Ipatiev Monastery has not been preserved, as during the time of Peter the Great, most of them were melted down to make cannons. The current bells belong to different periods. The last bell, "Tsar Mikhail," was cast in 2006 in honor of the 400th anniversary of Tsar Mikhail Fyodorovich's accession to the Russian throne and was gifted by Michael, Prince of Kent.