The church is first mentioned in 1626 in the Pistsovye books of Kerekreysky V.A., which states: "The Church of the Intercession of the Most Holy Theotokos, and in the church are icons, candles, books, vestments, bells, and all church structures." The last mention of the old wooden Intercession church in Belgorod was in 1787. The clerical report of 1870 states: "The Intercession church is stone with a bell tower of the same type, built in 1791; chapels were arranged: on the south side in the name of St. Mitrophan of Voronezh in 1837, and on the north side in the name of St. Tikhon of Zadonsk in 1865, at the expense of the parishioners."

The church is located north of the Assumption-Nikolai Cathedral on Pushkin Street (formerly Battalionnaya). In 1837, new chapels were added to the southern facade, and in 1865 to the northern facade, giving the building a square shape.

This is an interesting example of architecture from the late 18th century. In the volumetric composition of the church, the two-light square of the temple with a cubic roof and a dome on a small square stands out, a four-tiered bell tower with diminishing tiers, set on a narthex, closed by late extensions, and a two-light five-sided apse. The centers of the northern and southern chapels are highlighted by triangular pediments and topped with gable roofs. In the architectural plasticity of the facades, a stylistic division is noticeable: the square of the temple and the central apse are executed in baroque forms, while the bell tower is typical of early classicism. In the northern and southern extensions, classicist techniques of the mid-19th century prevail.

In the second half of the 20th century, the church building was used as mechanical workshops. Restoration began in 1991, and by 1993, the center of the Marfo-Mariinsky Convent was transferred to the church from the village of Zimovyenki.