The history of the Holy Trinity Cathedral begins with the visit of the royal family to Yekaterinodar in the late 19th century. In 1888, the train carrying the royal family derailed, but fortunately, there were no casualties, only a few servants and ladies-in-waiting sustained minor injuries.

In 1889, after a prayer service at the Alexander Nevsky Cathedral, the City Administration decided to build a church with seven altars in the 113th quarter of the second part of the city. Representatives of the Administration, including V. S. Klimov and elder A. Erokhin, sent a telegram to the Sovereign, expressing their loyalty and informing him of their intention to commemorate the salvation of the royal family by constructing a church in honor of the holy patrons of the August family.

On November 6, 1887, a Royal gratitude was received. Soon, on April 20, 1896, the widow of the official, Yefrosinya Abramovna Shcherbinina, offered a plot for the church's construction and donated 2000 rubles, asking for a small pension and a cottage in return. The Duma accepted her proposal, and on October 3, 1899, the laying of the church took place. Architect I. K. Malgerb presented the design for the cathedral, intended for 1000 people.

Since 1902, a prayer house operated at the future church site, where Father Vasily Biryukov served. In 1902 and 1903, work was carried out on the construction of the bell tower and roof.

On June 29, 1904, the crosses were raised on the domes, and the altar of the lower church was consecrated in honor of St. Seraphim of Sarov. The church was planned to have altars: the central one in the name of the Holy Trinity, the right one in the name of St. Basil the Great, and the left one in the name of St. Euphrosinia. Later, the altar of St. Euphrosinia was moved to the lower church, and the left one was named after St. Seraphim of Sarov. Construction halted from 1905 to 1907 due to a lack of funds and dampness that damaged the icons. The City Duma allocated 15,000 rubles for the iconostasis, concluding a contract with master Strelkov and artist Safonov. All work was completed by the end of 1909, and on June 7, 1910, the church was solemnly consecrated. In 1911 and 1912, repairs were made to the lower church, which was consecrated on November 1, 1912. The church grounds housed a parish school and a city school.

Unfortunately, the church operated for only 20 years. In 1934, it was closed, but in 1942, with the permission of the occupying authorities, services resumed. After the war, the cathedral was closed again.

During its abandonment, the church lost its utensils, icons, furniture, and iconostases. Chandeliers and candelabras were sent to the City Executive Committee, and the fence of the cathedral still stands around the children's hospital on Turgenev Street.

Until 1972, the church housed a warehouse and a salting base. The frescoes were painted over with oil paint. Later, the building was used as a sculptural workshop for the Krasnodar Art Fund of the USSR. Many monuments of Krasnodar were created in the cathedral during those years.

In 1985, architect G. I. Bekbulatova described the condition of the cathedral: the facades were cluttered, the porches were destroyed, the frescoes were painted over, the roof was damaged, the doors did not close, decorative grilles and stained glass were lost, and the interiors and floors were in a neglected state.

In 1989, believers collected over 2000 signatures and achieved the return of the building to the Kuban Diocesan Administration. In 1990, the cathedral was returned to the faithful, and services resumed.

Since September 1, 2006, the Yekaterinodar Spiritual Seminary and a Sunday school for children have been operating on the cathedral grounds.

On September 16, 2020, the Archpastoral Council of the Kuban Metropolis decided to unite the Holy Trinity Cathedral and the Yekaterinodar Spiritual Seminary into a single Spiritual and Educational Complex.