The first church in Yeisk was the temple in honor of the Intercession of the Holy Virgin. Yeisk priest Maxim Prozorovsky described its history as follows: the first religious building in Yeisk was a prayer house dedicated to the Intercession of the Holy Virgin. In mid-1849, the city's residents appealed to His Grace Caucasian Jeremia with a request to allow the construction of this house according to the attached plan and facade. The plan was signed by the city chief Prince Golitsyn and architect Zhukovsky, and it had a resolution from Jeremia on top. In August of the same year, His Grace blessed the construction.

Receiving the blessing, the residents of Yeisk consecrated the site on September 1, 1849, in one of the squares on Greek Street and began construction. The building was modest and did not stand out for its grandeur or beauty, resembling a house of Eastern style. Its dimensions were 18 arshins in length and 14 in width, with a corresponding height. Covered with planks and surrounded by canopies, the house was built quickly and consecrated on October 1, 1850. It was a wooden building without a bell tower or paint, with a single altar in honor of the Intercession of the Holy Virgin.

In 1858, after the construction of the temporary Mikhail-Archangel Cathedral, the Intercession Church became a dependency of it, and its history was interrupted for a time. In 1864, by the order of Bishop Theophilakt of Caucasus, the church was renamed a parish church with a separate parish and clergy.

In the following years (1865 and 1866), the life of the parish was calm. However, on April 7, 1876, the wooden Intercession Church burned down due to careless handling of fire.

The residents of Yeisk appealed to the City Head with a request to temporarily use the old wooden building of the Mikhail-Archangel Church for prayers. A new project for the Intercession Church was also proposed, with construction estimated at 100,000 rubles. The City Duma decided to move the wooden building of the Mikhail-Archangel Church to Intercession Square until the new church was completed. In 1876, a wooden Intercession Church was built on a stone foundation and consecrated in the same year.

In 1907, a new church was built on the site of the old one, named the Old Intercession Church, as there was already a New Intercession Church in the city, built in 1890. The five-domed Old Intercession Church became a decoration of the city. It was made of stone and covered with iron. Next to it was a brick building of the church parish school, also covered with iron, as well as a small house for the caretakers and a wooden shed.