The architectural and archaeological remnants of the Transfiguration Cathedral are located in the center of the complex. The cathedral was built between 1595 and 1601 as a white-stone six-pillar three-apse temple with five domes, comparable in size and artistic quality to the Annunciation Cathedral.

Originally, the cathedral in honor of the Transfiguration of the Lord was constructed in the 1550s from wood on a stone foundation. From 1596 to 1601, a stone six-pillar temple with five domes and three altar projections was erected in its place. It was built on an earlier stone foundation, which has survived to this day and resembles the lower church of the Annunciation Cathedral. This space features four pillars and a wall with openings that separates the altar area, supported by barrel and cross vaults. The upper part of the building was destroyed in the 1930s, but even the remaining part allows us to judge the numerous reconstructions that the Transfiguration Church underwent.

In the 18th century, galleries were added to the cathedral on the northern and southern sides, which differed from each other. The southern gallery consisted of vaulted rooms at the level of the lower tier of the cathedral, connected to the main white-stone volume. The top of the gallery was flat and served as an open porch. The northern galleries were two-tiered. The first tier consisted of vaulted rooms with cross vaults, resting on white-stone bases of trapezoidal shape. The second tier has not survived and is currently being restored. According to historical data, this was a vaulted space under a single-pitched roof, serving as a corridor connecting the cathedral with the rector's house and the Church of St. Nicholas the Warrior. The eastern galleries began with a large ceremonial entrance. In 1901, an extension was made on the western side, spanning the entire width of the cathedral.

The Transfiguration Cathedral was destroyed in the mid-1920s during the struggle against religion. To this day, the basement floor with ceilings has survived. The walls of the foundation are made of white stone, with blocks smoothly hewn and tightly fitted together. The vaulted ceilings are also white stone, resting on the walls and two rows of square columns. The entire complex of these buildings is now being adapted for the Museum of Archaeology of the Republic of Tatarstan.

The first bell tower of the Spaso-Transfiguration Cathedral was wooden. The second, made of stone, existed until 1858 and was located to the northwest of the cathedral on the gallery connecting to the rector's building. Due to its dilapidated condition, the bell tower was dismantled. From 1858 to 1860, a new bell tower was built above the Holy Gates of the Varvarinskaya Church. Three tiers were added to the cubic volume with gates on the first floor and a church on the second floor. The second tier housed the bells, while the third contained the clock. Currently, the location of the bell tower is marked by a different color of paving stones on the sidewalk.