The church was built between 1842 and 1845 on Galkina Mountain, on the site of the old wooden Michael-Archangel church, erected in 1783. Local merchants Nikita Serafimov and Daniil Balaev participated in the construction. The church was consecrated on November 7 and 9, 1847. It was initially planned to be a cathedral, but this role was taken by the Trinity Church, built a little earlier, and the Archangel Church became a parish.

In the northern part of Bashkiria, this church remained the only functioning one, except for the period from 1937 to 1945. In 1937, the building was used as a grain storage, and the bell tower was demolished. In 1945, the church was reopened by priest Gavriil Zhelvitsky. Its restoration involved nuns who remained in the city after the closure of the Birsk Trinity Monastery in 1924. In the early 1950s, the grandfather of Patriarch Kirill, priest Vasily Stepanovich Gundyaev, served here.

According to resolution No. 390 of the Council of Ministers of the Bashkir ASSR dated July 19, 1976, the church was recognized as a monument of local architectural significance.

In 2002, major repairs of the church began: a new bell tower was built and the surrounding area was improved. However, it was reported that during the renovation, frescoes and decorative elements were lost. In June 2016, during a visit to Bashkortostan, Patriarch Kirill visited the church and held a service there.

On the church grounds, there is the diocesan sewing workshop 'Tavifa', a department of religious education and catechesis, as well as a missionary department.