In 1714, a stone church was laid in honor of the Entry into the Temple of the Most Holy Theotokos on the site of the abolished wooden church of Saint Nicholas the Wonderworker. It was consecrated in 1743, but the people continued to call it the Nikolsky Church.

The church was located just behind the walls of the Sophia courtyard, on a hill, at the Nikolsky ascent, and its volume closed the Trinity cape. Construction began even before Peter's decree of 1714, which prohibited stone construction in Russia, except for St. Petersburg. Work resumed only in 1724, and in 1743 the church was completed and consecrated. Its architecture reflected the features of the ancient Russian style of the 17th century, including a tent-shaped bell tower.

The church was rebuilt several times, with the final reconstruction completed in 1774. It had five altars: in honor of the Entry into the Temple of the Most Holy Theotokos, the Lord's Entrance into Jerusalem, Saint Great Martyr Demetrius of Thessalonica, Saint Great Martyr George the Victorious, and Saint Nicholas the Wonderworker. By the end of the 19th century, the clergy consisted of a priest and a psalmist, and the parish included 13 villages.

By the early 1890s, due to the small number and poverty of the parishioners, the church fell into extreme disrepair, and services were held rarely, as the southern side of the building had separated and threatened to collapse.

Bishop Justin (Polyansky) established a committee for the restoration of the church, entrusting the collection of donations and the conduct of works to the Tobolsk archpriest Alexander Grammatin. In 1891, the church was brought into decent condition, although not luxurious.

After the revolution, services continued in the church until the early twenties, but then it was turned into a garage for the UGB NKVD prison. In 1930, the city authorities closed the church, bringing it to an emergency state, and in the 1950s it was completely destroyed.