The Spaso-Transfiguration Cathedral, built in the 16th century, was originally wooden and located in the northwestern part of the monastery on an elevation. Surrounding the altar of the cathedral was the monastery cemetery.

The main wooden church of the wealthy Spassky Monastery was conceived as a majestic tower-type building with a small but high prayer hall. For this, the common type of church at the time, "of twenty walls," was suitable. The base was a quadrangular log structure, to which small rooms for the altar, sacristy, and vestibule were attached. These rooms were covered with three rows of diminishing kokoshniks and barrel roofing. The quadrangular log structure continued with an octagonal one, which in the 16th century was topped with a tent roof, culminating in an onion dome with a cross. The dome and neck were usually decorated with shingles and intricately carved aspen boards. The entrance was adorned with a high porch with a roof.

Over time, the Arzamas Spassky Monastery developed and became wealthier, replacing wooden buildings with stone ones. The first stone building in Arzamas was the Transfiguration Cathedral, the construction of which began in 1638 under the abbacy of Ion. He planned to build it on a large scale and signed a contract with the Moscow New-Spassky Monastery for the construction of the iconostasis. However, in the same year, Ion was transferred, and his successor, Abbot Cornelius, reduced the size of the church and the iconostasis. The cathedral was completed and consecrated no later than 1643.

The Transfiguration Cathedral had three altars. The central altar is dedicated to the Transfiguration of the Lord. A description of the monastery from the late 19th century mentions two chapels: on the right, the Dormition of the Mother of God, and on the left, St. Mary Magdalene. The inventory from 1763 mentions a chapel in honor of St. Varlaam of Khutyn.

After the October Revolution of 1917, the cathedral was sealed. In 1919, the community of believers signed a contract with the Arzamas Soviet for the transfer of two churches, including the Transfiguration Cathedral. However, a year and a half later, the authorities announced the liquidation of the monastery and sealed the churches. After petitions in 1921, the community was left with two churches, but soon the cathedral was confiscated. By 1924, the community only had the Church of the Nativity of the Mother of God. The Spassky Cathedral was used as a warehouse and later as an archive.

In 2015, after the cathedral was returned to the church, the archive left the building.