The brick Intercession Church was built in 1754 on the site of the oldest wooden church in the city, erected before 1667. Researchers note that there was a cemetery near the city’s Intercession Cathedral in the Kremlin in ancient times. In the 17th century, there were two wooden churches here: the Intercession Church and the Alexievskaya Church. In 1678, the Alexievskaya Church "stands empty without singing, and the cathedral priests do not serve in it"; it was soon dismantled. After that, the parishioners of the Intercession Church continued to honor the memory of Saint Alexius, the Man of God. The antimension of the destroyed Alexievskaya Church, with an inscription about its consecration in 1647, was kept in the Resurrection Cathedral. Until the early 19th century, near the summer Intercession Church of 1754, 50-70 meters to the west, there was a stone Church of John the Baptist built in 1773, which was dismantled in 1814 due to dilapidation. A chapel was built on its site, which was destroyed during the revolution. After the reconstruction of 1814-1816, the church had three altars: the main Intercession altar, as well as side altars of John the Baptist and Great Martyr Theodore Stratilates, in a spacious refectory built in those same years. Until the early 1990s, traces of frescoes depicting John the Baptist and Theodore Stratilates were preserved in the niches on either side of the main entrance.

The bell tower was erected in 1814-1816. Its spire was covered with English tin and gilded. A large bell, possessing a "approximately-sounding" tone, was cast thanks to the efforts of honorary citizen F.G. Popov. The bell tower and the domes of the Intercession Church, along with the bell towers and domes of neighboring churches, formed a unified architectural ensemble. In 1814-1816, the facade of the church was altered, and a new refectory with a bell tower was added with funds from F.I. and A.I. Kornilov. In 1848, thanks to the efforts of I.N. Kornilov, a fence with a church shop was built in the southwest corner. Under the places where the plaster has fallen off, traces of the original window frames in the Naryshkin Baroque style with figured pediments are visible. The high space of the main square, covered with a vaulted ceiling, contrasts with the low apses, which have cylindrical vaults transitioning into conches, and the original refectory with a semi-vaulted ceiling. The new refectory with four cross-shaped columns is covered by a system of vaulted ceilings on supporting arches, with troughs at the rounded corners. Fragments of glue painting from 1812, executed in the traditions of the second half of the 18th century, have been preserved in the square and the old refectory. Above the entrance to the narthex in the early 20th century, there was an image of the Intercession of the Mother of God, and on either side of the entrance doors outside, Saint John the Baptist on the right and Great Martyr Theodore Stratilates on the left.