The renowned art historian of the Russian North, V. P. Vygolov, used two randomly found materials from the Totma Local History Museum to date the Church of the Nativity of Christ. These were a manuscript by local historian and art critic D. M. Grigorov titled "The City of Totma. Historical Essay," created in the 1910s-1920s, and a brochure "A Guide to the Attractions of the City of Totma and Its Surroundings," published in 1916. Analyzing these sources, Vygolov established that the church was built in two stages with a significant time gap. The lower floor was constructed between 1746 and 1748, while the upper floor was built from 1786 to 1793. During this time, a bell tower was also erected, which unfortunately has not survived. The names of the architects who worked on the church remain unknown. Interestingly, the architect of the upper part of the building managed to harmoniously combine elements from different periods, making the structure appear cohesive despite the differences between the tiers. The name of the church's patron is also unknown, although there is a suggestion of a possible connection to merchant Alexei Neratov, which remains unconfirmed.

The Nativity Church, a masterpiece of Totma Baroque, was not the first church dedicated to this feast in Totma. It is known that in the early 17th century, there was already an ancient Nativity Church, next to which stood the Church of St. Nicholas the Wonderworker, and they shared a common clergy. The 1646 census mentions the reconstruction of the Nicholas Church: "In the same Yerzov Lane, the church is being rebuilt with two chapels, of Nicholas the Wonderworker and of the great martyr Paraskeva, called Friday." The reason for constructing a new building is not specified. It is also reported that there were five cells on the church grounds where elders and widows lived. The further fate of these churches is unknown, but it is presumed that they burned down in the fire of 1743. The wooden Nativity and Nicholas churches were recreated in a single stone building in the 18th century. The altar of the lower floor was consecrated in honor of the Nativity of Christ, while the upper altar became dedicated to Nicholas.

The Church of the Nativity of Christ was closed in the 1930s, and the bell tower with the church of St. Paraskeva Friday in the lower tier was destroyed. The interior decoration was almost completely lost, and the building was used for economic purposes.

In the 1990s, revival began. In 1995, the Nativity Church was transferred to the Vologda Diocese, and its restoration began. The consecration of the church took place in 1999. A significant event was the transfer of the relics of the patron of Totma, St. Theodosius of Sumarina. In 1988, for the 1000th anniversary of the Baptism of Rus, the Vologda Museum transferred the relics to the Vologda Diocese. Initially, they were located in the Lazarus Church of Vologda, and in 1994 they were ceremoniously transferred to Totma. Before the revival of church life at the Nativity Church, the relics were kept in the Trinity Church of the Zelenka settlement. Until September 2016, they were in the lower tier of the Nativity Church, and on September 15, 2016, they were transferred to the monastery founded by St. Theodosius of Spas-Sumorin.