This church was located between the Kazan Cathedral and the Church of the Descent of the Holy Spirit upon the Apostles. Its construction took place from 1752 to 1754 under the guidance of the builder Pafnutiy, who was buried here. From 1780 to 1790, there was an altar in the church in honor of the Nativity of the Prophet and Baptist John, built by the builder Serapion. By the early 19th century, the Intercession Church had fallen into disrepair, and a decision was made to build a new Holy Spirit Church, where the John the Baptist altar was later moved.

The first Divine Liturgy after the restoration of the church took place on the feast of the Intercession in 2004.