In 1664, with the blessing of the Rostov Metropolitan Ion Sysoevich, the first stone church of the monastery was built in the name of Athanasius and Cyril. After the construction was completed, the church was adorned with frescoes made by masters from Moscow. However, in 1670, the monastery suffered from a fire. In 1676, a warm church with a bell tower was added to the northern side of the cathedral, dedicated to Alexius, the Metropolitan of Moscow. The monastery was small and surrounded by a low stone wall only on the eastern and northeastern sides, while on the other sides it was bordered by residential houses and the Spaso-Proboinskaya Church. On the eastern facade of the monastery, facing Proboinaya Street, two small stone towers were built in the 18th century: one served as the Holy Gates, while the other housed a chapel in memory of the discovery of the miraculous icon of the Savior Not Made by Hands. On June 25, 1768, another fire occurred in the central part of Yaroslavl, after which a list of damages was compiled. The fire damaged both churches, the abbot's and brother's cells, the kitchen, the stable, the carriage house, the bathhouse, the cellars, and the fence. The total damage to the Athanasius Monastery was estimated at 1000 rubles. During the restoration work, the painting of the church of Saints Athanasius and Cyril was renewed, and the stone iconostasis was replaced with a wooden one. In the 1820s-1830s, significant improvements were made in the monastery: stone two-story abbot's quarters with a refectory were built by the northern wall, and two brother's cells were constructed by the eastern fence. Around 1825, a new iconostasis was made for the church of Athanasius and Cyril, and in 1831, the warm church was expanded and decorated with frescoes by the artist Timofey Medvedev. At the same time, the monastery received a 115-pud bell from the abolished Borisoglebsk parish, and the bell tower included a total of seven bells. In the post-revolutionary years, a parish community was registered at the monastery, which was mentioned for the last time in 1923. In February 1925, the monastery was closed, and part of the dilapidated property was transferred to the Church of the Savior on the City and other churches. In the 1930s, the city authorities dismantled the monastery's bell tower, and various enterprises were placed in the churches and cells, including the administration of a furniture factory, while people settled in the brother's buildings. In 2006, with the blessing of Archbishop Kirill of Yaroslavl and Rostov, the church of Saints Cyril and Athanasius became a seminary church, and the Spaso-Proboinskaya Church was also assigned to the seminary.