In May 1871, Grand Duke Mikhail Nikolaevich, who visited the Black Sea region as the viceroy of the Caucasus, proposed to build a permanent Orthodox church at the Dakhovsky post. The foundation stone of the church, planned as a two-altar structure dedicated to St. Michael the Archangel and St. Mary Magdalene, was laid on May 26, 1874, at the site of the former Navaginsky fortification in the center of the Dakhovsky post. On September 24, 1891, Bishop Agafodor (Preobrazhensky) of Sukhum consecrated the church, built in eclectic style according to the design of Moscow architect A. S. Kaminsky, in honor of the archangel Michael.

In 1934, the Mikhailovsky church was closed, and its building was handed over to the Sochi resort management for use as a warehouse. Services resumed on November 2, 1943. With the efforts of parishioners, the church was repaired, and the dome with the cross and the bell tower's tent were restored. In 1947 and 1948, Patriarch Alexy I of Moscow and all Russia, while resting and recovering in Sochi, visited the church multiple times and prayed at the altar during episcopal services conducted by Bishop Flavian (Ivanov) of Krasnodar and Kuban and Metropolitan Gregory (Chukov) of Leningrad and Novgorod.

In 1981, the church building was recognized as a monument of architecture. During the restoration carried out in 1992 and 1994 according to the project of Sochi architect F. I. Afuxenidi, the church regained its original appearance. On December 19, 1995, Bishop Philaret (Karagodin) of Maykop and Armavir laid the foundation for a baptistery next to the church, consecrated on May 12, 2008, by Metropolitan Isidore (Kirichenko) of Ekaterinodar and Kuban in honor of the Most Holy Theotokos and her icon "Iveron."

In 2007 and 2008, another restoration of the Mikhailovsky church was conducted. As part of this, a water blessing chapel-ciborium was built and consecrated on November 21, 2008, in honor of the Most Holy Theotokos and her icon "Life-Giving Spring." On November 23, 2011, Metropolitan Isidore of Ekaterinodar and Kuban consecrated a monument to the last Russian Emperor Nicholas II, installed a few meters from the southern facade of the church.