A place for the construction of a soldier's church of the Barnaul rifle regiment at the beginning of the twentieth century was allocated on the central city avenue, not far from the regimental barracks. The construction took less than two years, and since 1906 all those called up for military service from Barnaul took the oath in this church. Large-scale celebrations were held on the territory adjacent to the church.

Since the 1930s, when the church lost its crosses, a bell tower and internal paintings, it was either empty or used as a club - a military unit, and later a flight school. In 1992 Nikolskaya Church was returned to the Orthodox community. Over time, it was decorated with a new bell tower, gilded crosses and domes, which improved the acoustics of the service. The interior painting was done by the Barnaul artist Vladimir Konkov, the iconostasis was done by the Palekh icon painters.