The Church of the Nativity of the Virgin is one of the smallest churches in Novgorod, measuring 7.5 by 9.5 by 12 meters. There are no direct mentions of the construction of a stone church on the site of the previous place of worship in the chronicles, however, its construction is dated to the 30s of the 13th century. It is believed to have been built in 1226, when the father of Alexander Nevsky was in Novgorod and the election of the archimandrite took place.

The first measurements and studies of the Peryn Church were conducted in 1947 and 1948 by R. A. Katsnelson, who discovered fragments of 13th-century frescoes under a layer of brick. In 1961, architect L. E. Krasnorechyev completed the final restoration project, returning the church to its original appearance. Restoration work was carried out in 1962 and 1965, but the interior was not restored.

During the restoration, the original three-part covering of the church and fragments of frescoes in the window reveals of the drum were revealed. The walls, narrowing upwards, the pilasters, windows, and drum give the building a lightness and an upward aspiration. The church has three spacious entrances, and the slender dome columns create an impression of space and height, despite the small size of the temple. The foundation of the building consists of masonry from the pre-Mongol period made of limestone and thin bricks, laid on a lime mortar mixed with brick crumbs.

The cross crowning the church has a shape characteristic of the pre-Mongol period, known as the "dome cross with a crescent." This crescent, a stylized grapevine, is not related to Muslim symbolism but has Christian interpretations.

The Church of the Nativity of the Virgin in Peryn is one of the few preserved architectural monuments of the 13th century in Russia. The facades of the church, devoid of decoration and pilasters, anticipate the features of Novgorod architecture of the late 13th and the first half of the 14th century.

Currently, the church has been restored to its original appearance. After the restoration of the interior, Archbishop of Novgorod and Staraya Russa Lev consecrated it on March 10, 2001. In 2004, the first and so far only tonsure into monasticism took place.