Our ancestors referred to a dol as a low bank that would flood during the river's overflow. It is in such a lowland on the banks of the Vologda that the Bogorodsky temple stands. It is called "Lower" because upstream there was the Upper Dol, where there was also a church of the Nativity of the Virgin. Historians date the construction of the wooden church in the Lower Dol to the end of the 16th, beginning of the 17th century. Later, thanks to the efforts of parishioners, a stone church was built, and its main altar, dedicated to the Nativity of the Blessed Virgin Mary, was consecrated in 1779. The church also had altars in honor of Saint Nicholas the Wonderworker and the Vologda miracle worker, St. Gregory of Pelshma.

During the Soviet era, the Upper Dol church was destroyed, while the Lower Dol church was preserved, although there were plans to demolish it. However, specialists decided that building in a flood-prone lowland was impractical, but losing a strong building near the river, which was then an important transport artery, was also not advisable. The church housed a mirror production facility, a transport management base for river development, and a repair and mechanical workshop for the baking industry. After the last workshop left the church, it was recognized as a cultural heritage site of regional significance. Local historians believed that services could be resumed here, but there was no interest in the church. After a fire in 2008, when the church was left without a roof, hopes for its restoration nearly vanished.

The first decree of Bishop Ignatius Deputatov on the establishment of new parishes in Vologda was issued on June 10, 2014, four days after his appointment by the Holy Synod. Parishes for seven churches in the city were formed, and the Lower Dol church found itself in the most deplorable condition.