In the late 18th and early 19th centuries, on the banks of the Tom River, near the Epiphany Church, there stood a temple of the Tomsk Old Believers, which was destroyed during the reign of Emperor Nicholas I.

The community was legalized in 1907, and Tomsk became the center of the Siberian diocese, which included the Tomsk, Yenisei, Irkutsk provinces, and the Semipalatinsk region. The City Duma allocated a plot for the construction of an Old Believer church on the street now known as Yakovleva.

The laying of the church took place in August 1910, and the wooden church of the Assumption of the Blessed Virgin Mary was completed and consecrated on September 22, 1913.

The consecration was led by the first Tomsk-Altaic bishop Joasaph (I.S. Zhuravlev), who was assisted by eight priests, including the church's rector Fr. Trifon Sukhov (the future Tomsk-Altaic bishop Tikhon), the well-known diocesan figure Fr. Daniil Suvorov, and others.

The church periodicals of that time described the event as follows: "At 6 o'clock in the morning, the consecration of the water was performed, and then of the church itself... Thanks be to God, now the Old Believers of Tomsk rejoice. Approaching the church and hearing the powerful ringing of the bells, they are filled with delight and weep with joy, for what our ancestors could not even imagine has happened" (Church. 1913. No47).

The existing wooden five-domed church with a refectory and a tent-shaped bell tower continued to function even during the Soviet years, but was closed in 1941 and 1944 and used as a warehouse. During the Soviet era, it was one of the few functioning Old Believer churches in Siberia and the only one in the Tomsk region. The church was visited by Moscow and All Russia Metropolitans on archpastoral visits.

By the 400th anniversary of Tomsk, the church was restored and received the status of a federal architectural heritage site.