Perhaps in honor of the heir to the throne, future Tsar Alexei Mikhailovich, a wooden warm church dedicated to Alexius, Man of God, was built in the Spaso-Gennady Monastery in the second half of the 1630s. From 1751 to 1756, a brick Alexius Church was constructed in its place, located in the southeast corner of the monastery and connected to the monastery fence, which previously adjoined the northern and southern facades of the eastern part of the building but has not survived to this day.

During the Soviet period, the Alexius Church was converted into a collective farm office, with the first floor used as a grain storage and a warehouse for pesticides. A silage pit was dug on one side of the church, and tractor tracks appeared around it, as well as throughout the monastery.

On July 22, 2017, Bishop Veniamin of Rybinsk and Danilov consecrated the church in honor of St. Alexius, Man of God. Currently, daily services are held in the church.