The city was founded in 1757 during the reign of Elizabeth Petrovna. The first settlers, newly baptized Chuvash, named the city after one of their own. Soon, the first wooden church in honor of St. Michael the Archangel was built in Belebey. However, during the Pugachev uprising, the Chuvash joined the rebellion and burned the church around 1774. In 1781, Belebey became the district center of the Ufa governorate of the Orenburg province, and on the site of the burned church, a second wooden church dedicated to St. Michael the Archangel was erected.

After 35 years, the city was ready for the construction of a stone temple. The project began in 1815 when a book for collecting donations was issued by the Orenburg Spiritual Consistory. This was managed by retired sergeant Alexander Malzev. In 1820, Archpriest Dmitry Dmitriev was appointed to Belebey. The construction of the stone church was delayed; material preparation began in 1822, and the construction was completed in 1828. In November of the same year, the church was consecrated by Archbishop Ambrose II Morev.

The church was built in the style of classicism but resembled a rural church. The facades were designed strictly, and the roof featured a dome with lanterns. The bell tower was low and squat. The new stone church was built deep within the block, not on the site of the old church. According to various accounts, a memorial sign was erected at the site of the former church, which was later replaced by a chapel. At the end of the 19th century, a brick chapel in the Russian style appeared on the site of one of the old churches, which has survived and is located opposite the current church.

In 1879, the St. Michael the Archangel Church became a cathedral. In 1915, parishioners decided to expand the church by reconstructing it into a three-altar structure in the Russian-Byzantine style. Merchant Mikhail Yagodkin made the first contribution, but the reconstruction did not take place due to historical events.

The church was closed during the first five-year plans, the bell tower was demolished, and the building was used as a warehouse. In 1988, for the 1000th anniversary of the Baptism of Rus, the building was returned to the faithful and restored for worship. The dome part was well restored, but the bell tower was recreated not in its original form.

Today, the Mikhailovsky temple is located in the center of the historical part of Belebey, surrounded by monumental buildings. In 1998, a second altar was consecrated in the church in honor of the Vladimir Icon of the Mother of God. Among the church's relics was an image of St. Seraphim of Sarov, as well as icons with particles of the relics of various saints.