On May 18, 1820, the construction of the Protection Church began, with the first stones laid in its foundation. By 1821, the winter single-domed church was completed. From 1827, the temple began to be painted by Timofey Medvedev. On July 21, 1828, the Archbishop of Yaroslavl and Rostov, Avraamy, consecrated the church in honor of the Protection of the Holy Virgin. In the same year, a 60-meter four-tiered bell tower was built above the Holy Gates adjacent to the church.

In July 1918, during the suppression of the White Guard uprising in Yaroslavl, the bell tower was destroyed by artillery fire. After the monastery was closed, the Protection Church continued to function as a parish for another three years. In September 1921, the church was closed, and the iconostasis, kiots, three altars, and three sacrificial tables were destroyed. During the Soviet era, the church building housed a library, a planetarium, and a secondary school called 'Provincial College.'

In May 2011, the building was returned to the monastery. In July of the same year, extensive renovation work began, including the dismantling of the reinforced concrete structures of the dome, walls, and ceilings. During the work, frescoes from the late 19th century were discovered, miraculously preserved.

On October 13-14, 2012, the all-night vigil and Divine Liturgy were held for the first time in the Church of the Protection of the Holy Virgin. In 2016, carved Royal Gates were made for the church's iconostasis, and in 2017, the creation of carved details for the iconostasis itself began.