The first mention of wooden churches of the Epiphany and St. Nicholas the Wonderworker in the settlement of Lyaly appears in the survey book of 1608. The census book of the Yaren district from 1648 also mentions these churches, but the Nicholas church already has a tented roof. It is noted that the churches have icons, books, candles, vestments, church vessels, bells, and all church property acquired with the funds of the peasant community.

The census book of 1678 mentions only the Epiphany church without specifying its type. Reports on the churches and priests of Yaren and the district from 1798 again mention two Lyaly churches, which burned down on May 8 of the same year. According to the Clerical report of the Lyaly Epiphany church for 1907, the existing stone church was built between 1852 and 1856 to replace the wooden one, which, according to tradition, was contemporary with the churches in Ust-Vym. It is likely that the residents of Lyaly managed to restore only one of the burned churches, which was contemporary with the Mikhailo-Arkhangelsk church (1795-1806) in Ust-Vym. The stone church had three altars: in the upper cold church in the name of the Uncreated Image of the Savior (consecrated on September 25, 1857), in the lower warm church on the right in the name of the Epiphany of the Lord (consecrated in December 1857), and on the left in the name of St. Nicholas the Wonderworker (consecrated in June 1888).

The Epiphany church was the last to be closed in the Komi ASSR at the end of 1941 amid persecution of the church. After its closure, it was used as a warehouse. In 1992, the building was transferred for free use to the local Orthodox community, and by the Resolution of the State Council of the Republic of Komi dated March 24, 1999, it was returned to the Syktyvkar and Vorkuta diocese of the Moscow Patriarchate of the Russian Orthodox Church. The project for the restoration of the architectural part of the building was developed by architect A.L. Smyshlyaev from the design institute "Spetsproektrestavratsiya", Moscow.