The Transfiguration Church became the first temple built in Gorno-Altaisk in modern times. It can be considered the successor to the main church of the central missionary station of the All-Merciful Savior, which was previously located in Ulala.

Before the construction of the church began, the community and city authorities engaged in lengthy negotiations. The authorities were reluctant to allocate a plot within the city, especially near a school. However, by 1988, a compromise was reached, and with the help of the Biysk Holy Assumption Parish, the construction of the Transfiguration Church began between Trudovaya and A. Matrosov streets. The plot was bequeathed to the Church by one of the parishioners. On August 30, 1988, the rector of the parish, Priest Rostislav Kirashuk, arrived in Gorno-Altaisk, and services began to be held regularly, first in a prayer house, and from October 24, 1989, in the church.

The Great Consecration of the Transfiguration Church was performed by Bishop Tikhon of Novosibirsk and Barnaul on August 18, 1991.

In 1994, the Seraphim of Sarov Baptistery was built, and in 2008, the Sunday School building. By the twentieth anniversary of the Church of the Transfiguration of the Lord, the temple was renovated, and the territory was improved.

Interestingly, the church has an architectural feature: it is not strictly oriented along the east-west axis. This is due to the fact that the building was integrated into a residential area with limited space. Later, utility buildings were erected on the site of the neighboring estate purchased by the parish.