In 1888, construction began on a new three-altar church on the site of the old wooden church. By 1896, thanks to the efforts and donations of parishioners and benefactors, a majestic stone church with three altars, a bell tower, and a fence was erected in Mikhailovsk, Sharlyk. The largest bell weighed 366 poods and was used during holidays, in case of fires, to gather residents, and in bad weather for travelers. The tongue of the bell weighed 17 poods. The main altar was consecrated in honor of Saint Archangel Michael on October 13, 1896, the right altar in honor of Saint Nicholas the Wonderworker on October 26, 1898, and the left altar in honor of Saint Prince Alexander Nevsky on May 21, 1901. The cost of constructing the church was about 70,000 rubles, and the iconostasis cost 12,000 rubles. In 1909, at the initiative of the church council created by the senior priest Fr. A. Polotebnov, the church was painted by artist Dmitriev from Orenburg for 5,100 rubles.

In 1932, the church was closed, the crosses were removed, the bell tower and dome were destroyed, and the building was repurposed as a club.

In 1993, the church building was returned to the church. At the time of transfer, it was in a state of disrepair and had not been renovated for a long time. In March 1993, the doors reopened for parishioners, and on Easter, the first service was held in the Church of Archangel Michael, conducted by schemamonk Seraphim Tomin, who came from Orenburg. This event brought joy to the believers and all the residents of Sharlyk.