The Church of the Intercession and Nativity of the Holy Virgin from Prolom served as the cathedral church of the Intercession Men's Monastery, located in the southwestern part of the Okolny town, near the Intercession Tower, named after the monastery. According to some sources, the church was built in 1399. The first mention of the monastery in chronicles dates back to 1544, when a fire damaged the Intercession Monastery and Yakimanskaya Street.

In 1582, after the siege of Pskov was lifted, the townspeople led by Voivode Ivan Petrovich Shuisky rebuilt the Intercession Church, adding a church in honor of the Nativity of the Holy Virgin. A classic Pskov bell tower was erected between the two churches. The church became a monument to the courageous defense of the city, where a synodic with the names of those who died during the siege was kept.

The main shrine of the church was the miraculous icon of the Mother of God of Pskovo-Intercession, before which a lamp always burned. On the silver-gilded robe, there was an inscription about Elder Dorotheus and the attack of Stefan Batory's troops on Pskov. In 1764, the monastery was abolished, and the Church of the Intercession and Nativity of the Mother of God was left without a parish but with a salary.

In 1813, the church was assigned to the Church of Nikita Gusyatnik. In 1847-1848, the church was rebuilt. Instead of the demolished bell tower, a bell tower with five bells was erected with donations, and the narthex was expanded. In 1912, an employee of the Pskov Archaeological Society, V.I. Ozeling, discovered and cleared the monastery's underground passage leading from the courtyard of the Intercession Church to the Intercession Tower and Batory's Prolom.

On May 5, 1936, the church was closed. During the German-Fascist occupation of Pskov, the church was damaged. The miraculous icon of the Mother of God of Pskovo-Intercession was taken away by the occupiers and was only found in 1970. In the summer of 2000, German Chancellor Gerhard Schröder handed over the icon, purchased from private owners, to Russian President Vladimir Putin. On September 7, 2001, the icon returned to Pskov and is now located in the Trinity Cathedral of the Pskov Kremlin.

In 1960, the church was placed under state protection, and in 1961-1964, restoration was carried out, returning the building to its original appearance. The church is very compact: its length with the narthex is 17 meters, and its width is 15 meters.