On March 7, 1905, Archbishop Agafodor appealed to the head of the Kuban region with a request to allocate a plot for the construction of a church in the village of Armavir. In 1908, the volost administration granted permission for construction on the condition of raising at least 30,000 rubles. On December 12, 1910, a document titled "Resolution of the village assembly of Armavir" was drawn up, signed by 62 participants, which designated a plot for the construction of the temple. The site was chosen at the intersection of Khotorskaya and Malominskaya streets (now S. Razin and Lunacharsky streets) in a modest area, away from the center.

Project work began on May 28, 1912, under the guidance of architect G. I. Akopzhanov. The construction was overseen by priest Leonid Dmitrievsky. On August 3, 1912, the laying of the prayer house in the name of the Holy Trinity took place. By September 2, 1914, the exterior work was completed. In 1915, against the backdrop of rising patriotic sentiments, donations increased, and the architect designed a church instead of a prayer house. The construction of the church was completed on April 28, 1916, and it was consecrated on May 26, 1916.

The first rector of the Holy Trinity Cathedral was priest Alexander Ukolov, who was shot during the Civil War on November 7, 1916. In the 1930s, of the five churches operating in Armavir, only the Holy Trinity Church remained, while the others were destroyed. However, even in this church, the authorities set up a warehouse.

A significant milestone in the history of the cathedral is associated with rector Leonid Dmitrievsky, who served in the church from 1942 to 1950. The church resumed its work during the German occupation. After the liberation of Armavir on January 24, 1943, Father Leonid organized a collection of donations for the Red Army and conducted reconstruction and major repairs of the church. He was awarded the medal "For Valorous Labor during the Great Patriotic War." In 1950, the rector became archpriest Alexander Volkanovich, and in 1956-1957, priest Georgy Stroyev. Rector Mikhail Samoylenko served in the church from 1964 to 1985.

Since 1991, the rector has been candidate of theology archpriest Sergey Tokar, the dean of the churches of the Armavir district. In 1993, the Armavir Orthodox Social Institute was established at the church. In 1995, the Holy Trinity Church was granted cathedral status.