The Church of the Exaltation of the Holy Cross was built in 1893 with the blessing of the famous missionary, Bishop Dionysius Khitrov of Ufa. The consecration of the church was attended by missionary priest Yevgraf Evaresov, who later held discussions with Old Believers here and was canonized as a holy martyr. The first rector was Archpriest Nikolai Kotelnikov, whom the parishioners regarded as a "good shepherd and a good father." He is buried at the altar of the church next to the church warden and main benefactor, merchant Trofim Kozlov.

Before the revolution, the parish of the Church of the Exaltation was one of the largest in Ufa, mainly consisting of workers. The church had a charitable organization that provided assistance to the poor residents of Nizhgorodka and families of soldiers during World War I. There was also a church parish school.

When Father Nikolai Kotelnikov had a deaf-mute son, he, concerned for his fate, decided to help other children with such disabilities by opening a school for the deaf in 1902 with charitable funds. One of the first donations for this cause came from Saint John of Kronstadt. The Empress Maria Feodorovna's charitable organization sent a specially trained teacher from St. Petersburg for the school. During World War I, the school became a military hospital with 94 beds. In 1914, a church was added to the building in honor of Saints Hermogenes and Nicholas, for which funds were donated by Nicholas II.

During the Soviet era, parishioners of the Church of the Exaltation kept vigil at the church to prevent its closure. From 1933 to 1937, the church served as the cathedral for Bishop Rufin Brekhov, who headed the Ufa diocesan council of autocephalous Old Church communities. After his arrest and the church's closure, the building was repurposed as a warehouse for mineral fertilizers. At the request of the faithful, the church was reopened in 1942.

For organizing the collection of donations for the front, rector A. Gorin and church warden M. Chumakova were awarded medals for "Valiant Labor in the Great Patriotic War." M. Chumakova hired Nikolai Chigvintsev as a watchman, who later became known as the Reverend Moses of Ufa. This was his first place of church service, from where he moved to the Sergiev Cathedral. The fir tree at the altar of the church was planted by his hands. At different times, hieromonk Peter Ladygin, archimandrite Panteleimon Stepanenko, igumen Sophrony Sharobirov, igumen Ilya Bobrovnikov, and priests Arkady Marinin, Theodor Troitsky, Igor Markov, and others served here.

During the Soviet period, when most churches were closed, the Church of the Exaltation remained a pilgrimage site for believers from many villages and settlements in the Ufa diocese. In 1994, the Exaltation of the Holy Cross Annunciation Monastery was opened on the church grounds, and after its relocation to Sterlitamak in 1998, Archpriest Roman Khabibullin established a brotherhood for the homeless and a social shelter here.