The construction of the cathedral lasted three years, and in 1838 the rough finishing of the church was completed. On September 7, 1840, the right chapel was consecrated in honor of the Nativity of the Most Holy Theotokos, on January 18, 1841, the left chapel in the name of Saint Nicholas the Wonderworker, and on May 31, 1841, the main altar in the name of the Holy Life-Giving Trinity.

Half of the sacred items: bells, books, and icons were transferred from the Mikhailo-Arkhangelsky Church to the Holy Trinity Cathedral. In the second half of the 19th century, a new city center formed around the cathedral, and the square around the church was named Trinity Square. The construction of the cathedral was overseen by local official of the zemstvo court A.R. Vatlashev. In 1863, the main bell weighing 333 poods, about 5 tons, was installed in the bell tower. In 1880, the cathedral was painted.

In the early 20th century, the cathedral was equipped with electric lighting from the first power station in Birsk, which also served the Konovalov house. In 1914, a part was added to the cathedral from the side of the bell tower. The Holy Trinity Cathedral was often depicted on postcards as a symbol of the city.

In 1937, the Bolsheviks closed the cathedral, and in the same year, the bell tower was demolished. The main bell was removed and sent to Ufa, but it never arrived. Its fate is unknown; it may have been sunk in the Belaya River. The bricks from the bell tower were used to build Secondary School No. 2, now the Faculty of Technology and Entrepreneurship. The crosses were removed from the cathedral, and the building was converted into the Aurora cinema. In 1932, part of Trinity Square was allocated for Lenin Park.

In 1956, the dome began to leak, and local authorities decided to solve the problem radically by replacing it with a gable roof. In 1963, a public museum of the city was opened in the cinema building, which operated intermittently until the late 1980s. The lack of major repairs led to the destruction of the church, and attempts at restoration were unsuccessful.

In 1992, the cinema was closed due to the emergency condition of the building, and it was decided that it would be cheaper to build a new cinema. The former cathedral building was in a deplorable state: the roof leaked, and the windows were broken. There were no funds for restoration, and the building was conserved. In the 1990s, its future was being decided.

In 1994, discussions about restoration resumed, but funds were insufficient. In 1996, ideas for using the building as a historical museum or for other purposes were discussed. In 1997, the building was transferred to the Ufa Diocese.

In the 2000s, restoration of the cathedral began. In 2007, the restoration of the dome started, and four frescoes of the evangelists were discovered. In 2008, work was suspended. In 2012, the issue of restoration was raised again. On June 3, 2012, Bishop Ambrose held a prayer service in the cathedral, marking the beginning of its revival.

In January 2013, restoration work began. On April 3, 2013, Bishop Ambrose laid the bell tower's foundation. On June 8, 2013, the main dome was installed, and 12 bells were brought. On September 9, 2013, the dome and cross were raised to the bell tower, and the cross was also installed on the main dome of the church.

On September 14, 2013, in honor of the 350th anniversary of Birsk, a procession to the cathedral took place, where a water blessing service was held, and an akathist was read. On January 8, 2015, the first Liturgy in the restored cathedral took place after 78 years, and services became regular.

In July 2017, the Birsk Diocese was established, and the Holy Trinity Cathedral became its main church.