The stone church of the Transfiguration of the Lord was laid in 1795. Irkutsk merchants Stefan Ignatiev and Ivan Sukhikh, who donated 6,000 and 3,000 rubles respectively for its construction, requested the creation of the Transfiguration church from Bishop Veniamin Bagryansky of Irkutsk and Nerchinsk. The bishop, in turn, contacted the Irkutsk governor Illarion Timofeevich Nagel and sent a petition to the Holy Synod to obtain permission to establish a parish. A response was received quickly, and a site for construction was allocated in the same year.

It is believed that the church's design was entrusted to architect Anton Ivanovich Losev. Although details of the construction are unknown, it is likely that blacksmiths and craftsmen from the Rabochedomskaya sloboda participated in the work, providing iron products for the church from their materials.

On August 10, 1798, the right Ilyinsky chapel of the church was consecrated, and a new Transfiguration parish was formed. It was allocated 41 households from the Cross Exaltation parish, 70 households from the Vladimir parish, and 84 households from the Annunciation parish, totaling 195 households, which amounted to about 800 parishioners. The left chapel in honor of the first martyr and archdeacon Stephen was consecrated on September 8, 1802. The main church in honor of the Transfiguration of the Lord was consecrated on August 6, 1811.

In 1849, with funds from the honorary citizen of Irkutsk, Yefim Andreyevich Kuznetsov, a church fence, a sacristy, and a porch on the north side of the church were constructed, and the wooden roof was replaced with an iron one.

The church was frequently visited by the Governor-General of Siberia Mikhail Mikhailovich Speransky and the Decembrists who were in Irkutsk. From 1845 to 1855, Decembrists Sergey Grigorievich Volkonsky and Sergey Petrovich Trubetskoy lived in the parish with their families. The daughter of the Volkonskys, Elena, and the daughter of Decembrist Mikhail Kyukhelbekker were married in the church. Here, the Decembrists Pyotr Alexandrovich Mukhanov and Nikolai Alexeyevich Panov were also buried.

Next to the church was a parish school opened with funds from N.L. Rodionov. On the opposite side of the street was a girls' orphanage run by E.M. Medvednikova, whose wards also attended this church.

According to archival data as of October 1, 1937, the Spaso-Transfiguration parish remained the largest of the three active Orthodox churches in Irkutsk, with 1,505 parishioners.

During the Soviet era, the church building housed an archive and a book depository. Outside, the church lost two side extensions adjacent to the porch, the sacristy, and the watchman's lodge.

Worship services were resumed in 2000.