By the end of the 19th century, many churches and monasteries were built in Russia, including Siberia, in honor of St. Nicholas. In the early 20th century, the construction of such churches continued, and Barnaul was no exception. During this time, the Pokrovskaya Church was built in the Zaychanskaya Sloboda, the Trinity Church in the hilly part, the Church of the Elevation of the Holy Cross, which is now a planetarium, as well as churches in honor of the Kazan Mother of God and St. Innocent of Irkutsk on the grounds of the women's monastery. Wooden churches were built in Ostrozhny Lane and in the prison castle. The streets of the city were adorned with several chapels designed by architect Ivan Nosovich, including a wooden chapel at St. Nicholas' spring.

On the central street of Barnaul, Moskovsky Avenue, a soldiers' St. Nicholas Church appeared. In the early 20th century, there was a rule that soldiers' churches should be built in locations where Russian troops of at least a battalion were stationed. Barnaul housed a rifle regiment, and the military department allocated 36,000 rubles for the construction of the church, while the project for a brick church accommodating 630 people was approved by Emperor Nicholas II.

On April 18, 1903, the city council allocated a plot for the church's construction at the corner of Moskovsky Avenue and Second Altai Street. In the spring of 1904, the site was consecrated, and the first stone was laid. Construction progressed quickly due to funding and the participation of soldiers and local residents. By December of the same year, the walls and roof were completed, and in February 1906, the church was consecrated. Here, recruits took their oaths, and local residents visited the church for prayers.

The St. Nicholas Church was visible from all sides, and folk celebrations were held on its grounds, such as the commemoration of the 100th anniversary of the Battle of Borodino and the 300th anniversary of the Romanov dynasty. In the 1930s, the church met the fate of many others: the bell tower and dome were destroyed, and the building was used as a military club. In 1992, the church was returned to the Russian Orthodox Church, and services resumed.

Unfortunately, all the frescoes and icons were destroyed, but the church retained some ancient icons, including an image of the Most Holy Theotokos, saved from destruction. The church also houses a bell made in 1903. The St. Nicholas Church is gradually being restored: the interior painting has been completed, a new iconostasis has been installed, and a bell tower has been built. There are plans to erect a dome to improve acoustics.

On June 4, 2006, the church celebrated its centenary. The day before the celebration, workers installed dome drums on the tower. On May 21, 2007, Bishop Maxim consecrated new crosses for the church.