The Holy Trinity Church in Ulan-Ude was built in 1770 from wood, and between 1798 and 1809 it was rebuilt in stone. The construction was initiated by merchant Vasily Pakholkov and completed by merchant Afanasy Naletov.

This church became the third stone temple in Verkhneudinsk after the Odigitrievsky Cathedral and the Spasskaya Church. Initially, it had two chapels. The main, "cold," chapel was consecrated in honor of the Holy Trinity in 1816, while the "warm," northern chapel was dedicated to Saint Innocent, Bishop of Irkutsk, in 1818. Before the revolution, the Holy Trinity Church was affiliated with the Odigitrievsky Cathedral.

After the closure of the Odigitrievsky Cathedral in 1929, services were moved to the Holy Trinity Church. In 1930-1931, the clergy faced serious trials when almost all were arrested on false charges of counter-revolutionary activities.

Despite this, the church continued to function even after many Orthodox churches in Buryat-Mongolia were closed in 1932. It remained active until 1940, as clergy and parishioners from other closed churches in the city came here.

After its closure in 1940, the church building was turned into a film distribution warehouse. Later, when the cemetery was transformed into a city park, a dance floor was added to the altar of the church. There were plans to create a museum of architecture in Ulan-Ude, but the idea was not realized, and the church began to deteriorate. Even after the resolution of the Council of Ministers of the Buryat ASSR on September 29, 1971, regarding state protection, the situation did not improve.

Since spring 1988, the Orthodox patriotic community "Salvation" along with the Buryat branch of the All-Russian Society for the Protection of Monuments and the Scientific and Production Center for the Protection of Monuments began repairs and restoration. In 1988, the church was transferred to the Russian Orthodox Church by the resolution of the Council of Ministers of the Buryat ASSR and the order of the Ministry of Culture of Buryatia in 1991. In 1996, by the order of Ulan-Ude Mayor V.A. Shapovalov, the territory of the former cemetery, which had become a city park, was handed over to the Holy Trinity Church.