On the eastern side of the main square of the monastery rises a massive bell tower over 32 meters high. Its main part, built in the second half of the 16th century, is a powerful wall with two low arches for bells on the second tier and two wide stone domes. Inside the bell tower, the bases of the domes are not visible now, as they are at the junction of the ancient and more modern parts. The lower tier of the bell tower housed a church, originally consecrated in the name of the Origin of the Honorable Wood of the Life-Giving Cross of the Lord, and in the middle of 1860, in the name of the Mother of God of the Caves. In the late 17th century, a chapel was built on the southern side in honor of Alexander of Svir. In the early 19th century, the bell tower underwent significant changes: in 1808-1809, the domes were dismantled and a new tier with a three-bay arcade was added. The project for the extension was developed by the clerk of the Archieral House, Mizerov. By 1824, all work was completed, and a rotunda in the classical style with eight columns and a dome, designed by architect P. Ya. Pankov, appeared. The clock, previously located on the Holy Gates, was transferred to the bell tower. Fragments of paintings from different eras have been preserved in the interior of the bell tower, the earliest of which date back to the late 17th century and are located in the chapel of Alexander of Svir. The church is distinguished by fresco iconostases, rare for Yaroslavl but common in Rostov churches. Due to irregular heating, the paintings often deteriorated and were repainted, which happened four times in the 19th century. The upper tiers of the bell tower were severely damaged during the White Guard uprising of 1918, but restoration work was carried out in the 1920s and 1950s, and the bell tower reopened to the townspeople. In 1991, the bells, which had been separated for a long time, were returned to it. The original bells have not survived, so they were replaced with specimens from the museum-reserve's collections. Currently, the bell tower houses eighteen bells, cast in the 16th and early 20th centuries in St. Petersburg, Yaroslavl, Holland, and Pskov. The largest of them weighs about 115 poods. The bell tower is once again fulfilling its function, regaining its status as the first bell tower of Yaroslavl.

The church under the bell tower of the Spaso-Preobrazhensky Monastery was originally consecrated in the name of the Origin of the Honorable Wood of the Life-Giving Cross of the Lord. In the 1680s, under the archimandrite Alimpius, it was decorated with paintings that were updated twice in the 19th century. Some fragments of 19th-century painting have been preserved on the eastern wall, separating the bright space of the church from the dim altar. The wall depicts an iconostasis with local, festive, deesis, and prophetic tiers. The local tier features images of Alexius the Man of God, the Tikhvin Mother of God, the Crucifixion, and the Origin of the Honorable Wood. Such paintings were common in Rostov churches of the time of Ion Sysoevich but are rare in Yaroslavl. Similar iconostases were also found in the Yaroslavl churches of Peter the Metropolitan and the Vladimir Mother of God. On the wall of the southern chapel are depicted Nicholas the Wonderworker, the Mother of God of the Caves, the Almighty on the throne, and the Yaroslavl princes Fyodor, David, and Konstantin, while in the second tier, the Feasts, in oval medallions, the apostles with scrolls. In the lunettes above are depicted the Praise of the Mother of God, Queen of Heaven, and the Sign. In 1824, by the order of Archbishop Abraham, a bronze iconostasis was installed in the church. In 1860, the painting was repainted by the order of Archbishop Nil, who wanted to make the church his burial place. The walls, except for the altar barrier, were re-plastered and painted by artist Yegor Konstantinovich Diakonov in an academic style. The vault depicts the New Testament Trinity and seven angels with instruments of the passions, while on the walls, the Transfiguration, St. Nil, St. Silvester, and Yaroslavl miracle workers. After the completion of the restoration on October 30, 1860, the church was re-consecrated by Archbishop Nil in the name of the Mother of God of the Caves. In the 1970s, the Caves Church was restored under the guidance of V.I. Vasin.