On April 1, 1808, the Tobolsk archpriest Father Peter Felitsyn informed the Samarovo clergy about collecting subscriptions from residents for the construction of a new stone church. The attached copy of the decree stated that the wooden Intercession church in the Samarovo pit was built long ago and needed repairs. Since the construction of new wooden churches was prohibited, it was decided to build a stone church in advance and raise up to two thousand rubles for this purpose.

At that time, there were 242 houses in Samarovo, 721 men and 725 women. The clergy consisted of two priests: Peter Protopopov and widower Fyodor Ilyinykh, deacon Ufim Naumov, and two sextons: Andrei Firsov and Yegor Loginov. The volost head Boris Gubin convened a meeting on July 1, 1808, where 115 peasants and yasak Ostyaks agreed to the construction and contributed 1584 rubles 30 kopecks. By November, the amount increased to 1955 rubles 25 kopecks, which were sent to Tobolsk through the Samarovo postman Gerasim Korepanov.

Architect Shanygin from Tobolsk proposed to build the church next to the wooden church, closer to Komissarskaya Mountain, and ordered trenches to be dug for the foundation. The peasants dug them, but Shanygin demanded they be deepened, explaining that a strong foundation was needed for a stone church. It is believed that the church was built in 1815, but this is not entirely accurate.

In 1843, archpriest Ioann Zaborovskiy, inspecting the Samarovo church, discovered that the iconostasis was unpainted and there were no icons, and services were not being held. In 1860, one of the merchants wrote that Samarovo had become an important port of Western Siberia, with a rich stone church.

From the early 1920s, the Intercession church began to deteriorate due to the anti-religious policies of the authorities. Believers were persecuted, and the church cemetery and the graves of priests were desecrated. In 1929-30, bricks from the church were used to build a canning factory. A 'Fishermen's Club' was built on the site of the church, which existed until 1970, after which the building became the gym of school No. 2. In the 1980s, the building was demolished, and a sports ground was established in its place.

In 1994, at the initiative of architect Nikolai Gordeev, excavations were conducted, and the foundations of the church were discovered. This became possible thanks to the meticulous work of architect Shanygin in 1808.

The idea of restoring the church received support from the head of the district administration Alexander Filipenko and the city administration. The work was led by Deputy Head of Administration Semyonov V. S. The restoration project was carried out by architect Kazakov from Novosibirsk.

On September 21, 1996, on the feast of the Nativity of the Blessed Virgin Mary, priest Sergey Kravtsov, who arrived in the city, served a prayer service, and parishioners cleared the old foundations, handing them over to builders to begin the restoration of the church, which had been destroyed during the Soviet era.