In 1816, on the northern outskirts of the city, at the site of the current First City Clinical Hospital, Sennoy Market, and the 'Intourist' hotel, a wooden church was built in honor of the holy apostle Thomas. Its construction was made possible by the efforts of Archpriest Kirill Russian from the Military Resurrection Cathedral and donations from the Cossacks, as well as funds left by Colonel Gulik.

Next to the church, a shelter was established for wounded and infirm Black Sea Cossacks and Cossack women. Over time, the building fell into disrepair, and it was decided to renovate and expand it. However, at the initiative of Major General Zavadovsky, it was decided to build a new, more convenient and beautiful building for the church and shelter.

In 1833, Captain Petrov, a military engineer, developed the project for the ensemble of the church, shelter, and hospital. In March 1843, a small consecration of the church took place, after which services began. The great consecration occurred in May 1844.

After the death in November 1853 of the appointed ataman Zavadovsky, who did much for the church and shelter, he was buried next to his wife, and a stone chapel with a gilded cross was erected over their graves.

Over time, buildings of the city hospital began to appear around the church and shelter. In May 1922, silver utensils were confiscated from the church under the pretext of helping the starving in the Volga region. Soon after, the church was closed, and its premises were used for storage and administrative services of the hospital, as well as a lecture hall for the medical institute.

150 years after the consecration of the church, its revival began. The first prayer service was held on July 17, 1994, and on December 5, 1999, Metropolitan Isidore of Ekaterinodar and Kuban performed the great consecration of the church.