The stone church in honor of the Blessed Virgin Mary was laid in the mid-18th century next to the old wooden church in the southern part of the city, along the road to Irkutsk. The funds for construction were donated by first-guild merchant Dmitry Barabanov, and the church was consecrated in 1773. Both churches had rich furnishings; for example, the wooden church had an iconostasis with a large icon of the "Last Judgment."

Initially, the Virgin Mary Church was a small two-tiered structure with a brick vault and an octagonal dome. The upper octagonal volume stood on a square base, which is characteristic of "Naryshkin" Baroque. Special attention was drawn to the decorative design of the facade, particularly the window frames of the lower tier with keel-shaped kokoshniks. The stonemasons were masters of their craft and used shaped bricks to create patterns. It is believed that the church was built by Moscow craftsmen in the brick style and was originally not plastered.

In 1862, at the request of Archbishop Innocent Veniaminov, the church was significantly expanded. A narrow refectory was added to the western side with northern and southern chapels connected by arched openings. The composition was completed by a massive three-tiered bell tower with a high spire. The facade decor of this part was concise. The reconstruction was carried out with the funds of the widow Anna Chepalova. In 1922, during the siege of Yakutsk by White Guard troops, the wooden Virgin Mary Church was destroyed and used as fuel.

During the Soviet years, the building of the stone church housed a laboratory for testing building materials, geological funds, and a geological exhibition-museum. From 1953, the Cosmic Ray Station operated there, and in 1962, the building was fully occupied by the Institute of Cosmophysical Research and Aeronomy of the Yakut branch of the Siberian Division of the Academy of Sciences of the USSR. The church also housed part of the scientific library's fund.

In 1997, the church was transferred to the Yakut Diocese, but it was only in May 2004 that the laboratories vacated the premises. By the blessing of Bishop Zosima, every Sunday, Archpriest Mikhail Pavlov and the believers read the Akathist to the Mother of God in the ruined building. By November 2009, it was possible to restore the external appearance of the church, and in December, the first service was held in one of the side chapels. In the central chapel, it is planned to install the surviving iconostasis from the John the Baptist Church, which is under restoration in Nizhny Novgorod. Two gilded carved iconostases for the side chapels were also made there, which Bishop Roman consecrated on October 14, 2013. Interestingly, the church that shared the iconostasis no longer exists; a hotel called "Polar Star" now stands in its place.