The Nicholas Church in Vladychnaya Sloboda was the eighth stone church in the city. However, since earlier churches, such as St. John the Baptist and the Sign of the Mother of God in Dyudikova Desert, as well as the churches of the Holy Spirit Monastery and the Kirillo-Ioanno-Bogoslovskaya Seminary Church on Solyany Dvor, have not survived, this church became the third oldest after the Sofia Cathedral and the cold church of Dmitry of Prilutsk on Navolok. This does not take into account the churches of the Spaso-Prilutsky Monastery, which were included within the city limits in 1993.

In 1781, the parish of the Nicholas Church was the third largest in Vologda, with 72 households. By 1892, it became the second largest by number of parishioners, reaching 847 people.

In February 1930, the church was closed, and the bells were removed. Initially, it housed exiled "kulaks" from the central and southern parts of the USSR, then the building was used as a toy factory and a felt factory. In the early 1990s, a community was established at the church, and fundraising for its restoration began. During the restoration of the Church of St. Nicholas the Wonderworker, new domes were installed and the brickwork inside was updated.

Today, the relics of St. Anthony, Bishop of Vologda and Great Perm, are kept in the Nikol-Vladychnensky Church, transferred here from the Sofia Cathedral on September 26, 1998.

The church stands out among other buildings of that time in Vologda due to its large size, five light drums, and two-column structure. It also features a high basement, external decor, a double apse, and a bell tower reconstructed in the 18th century, making it a typical urban church of Vologda from the second half of the 17th century.

G. K. Lukomsky described the church as follows: "The Church of St. Nicholas in Vladychnaya Sloboda is a very tall cube topped with five domes, which are closely and beautifully arranged. The forms of the shiny, elastic, bulbous heads are beautiful, and the drums are decorated with an arched belt with columns, as in the John Church in Dyudikova Desert." The decorative elements of the facades are expressed in large zakomaras, separated from the walls by a cornice. In the early 20th century, there were picturesque plaques depicting the twelve major feasts. The wall paintings also adorn the ascents to the upper church. The refectory, adjoining the church from the west, connects the church with an elegant tiered bell tower built in the mid-18th century. Its slender pillar consists of a square base, a high octagonal tier with bells, and two small octagonal sections topped with a cupola. Such tiered bell towers, which replaced ancient Russian tent-like structures in the 18th century, were characteristic of the architecture of Vologda and other northern cities of Russia at that time. The heaviest bell in the bell tower, weighing 2 tons, was cast in 1782 in Moscow by master Asan Strugovshchikov.

The altar part of the basement floor is interesting because it protrudes significantly to the east and ends with two semicircular apses, which is characteristic of several Vologda churches, such as the Church of Constantine and Helena, the warm church of Dmitry of Prilutsk, and the Assumption of the Mother of God.

The interior of the Nicholas Church is executed in the Baroque style. The wall painting was replaced by rich ornamental stucco that covered the vaults, arches, and columns. The church housed an iconostasis in the style of Louis XVI, combining painting, sculpture, and wooden carving.