The Church of the Annunciation of the Blessed Virgin Mary with a small refectory was built in 1748 on the site where a wooden church dedicated to the Kazan Icon of the Mother of God burned down three years earlier. The new warm stone temple was erected with the support of Moscow merchants Shchelyagins. The mosaic floor was created in the late 19th century with funds from parishioners, most of whom worked at the Pereslavl manufactory of Kuznetsov. Paintings on the interior walls and vaults were preserved, which were discovered under a layer of lime during restoration in 1999. Restoration artists from St. Petersburg cleaned, reinforced, and restored them. The conical dome of the Annunciation Church, like the dome of the Peter and Paul Church built at the same time, is elongated upwards and has a high narrow drum with a small cupola. Smaller drums with similar cupolas are located at the corners of the square base.

In 1900, a side chapel dedicated to the Meeting of the Lord was added to the main building. This was due to the fact that the small space of the church could not accommodate all the worshippers, as the residents of Pereslavl began to visit the Nikolsky Monastery en masse, despite its location in a swamp and inaccessibility due to washed-out roads in autumn and snowdrifts in winter. In the same year, with the funds of benefactors, a two-story sacristy was built on the southern side of the church. In 1902, a new side chapel in honor of All Saints was consecrated, and a two-story stone monastic building adjacent to the church was constructed.

The Annunciation Church was closed in the 1930s. The domes were destroyed, and the former church premises were converted into housing. After the monastery was returned to the Russian Orthodox Church, a major renovation was carried out in the Annunciation Church. With the funds of benefactor Viktor Ivanovich Tyryshkin, a gilded four-tiered iconostasis decorated with carvings was installed in the church. The icons for the iconostasis were painted by graduates of the icon painting school at the Trinity-Sergius Lavra. The relics of the Pereslavl saint, the venerable Cornelius the Silent, now rest in the church, and the Korsun Cross, ceremoniously transferred to the monastery on June 12, 2010, from the Pereslavl Museum, is also located there.