In the second half of the 17th century, during the construction of the stone fence of the monastery, a grand entrance known as the Holy Gates was created. The side facing the Volga was complemented by two round towers. In 1672, thanks to Yaroslavl merchants Semyon and Ivan Matveev-Sverchkov, the construction of the gates with the church was completed under the guidance of Abbot Gordian. In 1684, a southern annex was added with the funds of N. Ya. Lvov. In 1691, when a team of artists was decorating the Vvedensky Cathedral, the walls of the gates were also painted. On the second floor above the vaulted passage was a square one-domed St. Nicholas Church, which included the main room, a refectory, and an altar.

In the 18th century, the windows of the church and the facades were changed. In 1815, the tented roof was replaced with a hexagonal one with a spire. The church housed a gilded five-tiered iconostasis. During the stay of archbishops in the monastery, the church was used as a home church for the archbishop's cells.

From the late 1920s, the church was used by the new owners of the monastery, and in the 1930s it was adapted for housing. The passage from the Volga was bricked up and turned into a garage.

In the 1990s, the St. Nicholas Church was restored as a summer church and again became the home church for the monastery's cells. The Yaroslavl Museum-Reserve transferred royal gates and icons for it. The arch of the Holy Gates was painted by a team of masters under the guidance of A. Surikov, and the restoration of the preserved fragments of the frescoes was carried out by specialists from LLC YHM 'Restorer'.

On May 16, 1997, Archbishop of Yaroslavl and Rostov Mikhail consecrated the St. Nicholas Church. During the restoration, the interior of the church was painted, and an image of the family of the last Emperor of Russia, Nicholas II, appeared on the altar wall, made in honor of their canonization.