The history of the modern Holy Intercession Church is not fully studied. In 1792, Catherine II issued a decree for the resettlement of the Zaporozhians from the Sich to Tamani, Kuban, and the southeastern shore of the Azov Sea up to the city of Yeisk. On August 25, 1792, the Zaporozhian flotilla landed in Tamani. Upon arrival, a prayer service was held, which Colonel Savva Bely reported to the military judge A.A. Golovaty on September 12, 1792. The Cossacks revered the icon of the "Intercession of the Holy Virgin" as their patroness and always carried it with them. Their main goal was to build a church and dedicate it to the "Intercession of the Holy Virgin." Soon after landing, while settling in, the Cossacks began the construction of the church. However, due to a lack of funds and their small numbers, they could not carry out the construction, and then A.A. Golovaty took on the organization of the spiritual life of the Tamanians. Archival documents contain a request from Golovaty to Bishop Iov of Feodosia and Mariupol for the construction of a church dated July 1, 1794. Before the official request, Golovaty personally chose the site for the church, using materials from destroyed structures in Tamani. It is possible that the idea of building a stone church on the existing foundation emerged then. The Cossacks liked this place immediately after landing. Some old-timers claimed that the foundation was the base of a Turkish mosque, others believed it to be the residence of a Turkish pasha, while many thought it was a Christian structure. During the restoration of the church in 1911, it was indeed discovered that the ancient foundation did not correspond to the building erected on it.

The senior adjutant of the military headquarters, Orlov, in his book about the opening of the monument to the Zaporozhians in Tamani in 1911, wrote: "The Zaporozhians, after landing and looking around, noticed a quadrangular building with a Doric colonnade. It was deserted but well-preserved from Greek settlements. It could easily be adapted for a church, which was done. By 1794, the church was ready and consecrated in the name of the 'Intercession of the Holy Virgin.' Instead of a dome, the church had a lantern with a cross. Inside, it was a high and spacious room with an arched ceiling." Perhaps this was the very structure that Clark wrote about. The ancient foundation found in 1911 confirms that the Greeks also used this powerful foundation for their construction. It is possible that these were temple buildings of Tmutarakan. The quick completion of the construction draws attention, as the date of its completion on the marble slab of the church, installed after the restoration in 1911, indicates 1793, while the request was submitted by Golovaty in 1794. It is likely that the Greek building was adapted for the church in 1793 and consecrated. The construction was most likely carried out on the site of the Mstislav Church of the "Holy Virgin." Thus, the church ended up practically outside the stanitsa, in an inconvenient location for the residents, as the settlement moved in another direction, leaving the church on the outskirts.

The church was surrounded by a high stone fence, which was preserved until the Great Patriotic War. It had loopholes for rifles and two gates: to the north and west. In this reliable citadel, one could take refuge in case of danger. The parishioners took care of the church, bringing offerings not only in money but also in valuable items, sacred vessels, books, and church utensils. Golovaty, whose funds were mainly used to build the church, donated silver dishes, a censer, and a valuable tabernacle made by the regimental ensign K. Chizhevsky. Priest Demeshko brought with him to the church ancient books "Bible" and "Liturgion" published in 1691. The Church of the Intercession of the Holy Virgin became not only a symbol of Orthodox faith but also a cultural center for the settlers. Golovaty sought to preserve the cultural heritage of antiquity. By his decision, wooden pillars with a canopy were built around the church, under which ancient finds discovered in Tamani and on the Taman Peninsula were brought. This saved the finds from plunder and destruction. The importance of the found Tmutarakan stone, which testified to the location of the principality, was emphasized by Golovaty's intention to build a bell tower at the church gates and place the Tmutarakan marble stone of the deeds of Prince Gleb next to it. On March 28, 1807, two stones with images of saints were installed in the Holy Intercession Church.

However, the church in its original form did not survive. It was destroyed in 1855 by the French when their squadron approached Kerch. Five years later, the Cossacks restored the church on the same site. The clerk Fyodor Chepil built a stone bell tower in the churchyard in 1865 at his own expense, resembling a watchtower of the Cossacks. Six bells were placed on the bell tower, the largest of which weighed 200 poods. Orthodox services continued until 1910, after which it was decided to restore and renovate the church to its original form. On October 1, 1911, the Church of the Intercession of the Holy Virgin was consecrated again.

Pushkin and Raevsky visited the Holy Intercession Church, Suvorov listened to the ringing of the bells, and Lermontov lit a candle before leaving for war. In the 1850s, Saint Ignaty Bryanchaninov served as the rector here for two months. Archival data indicate that the Intercession Church housed cultural and historical monuments of antiquity found in Tamani in the 19th and early 20th centuries, the fate of many of which remains unknown.

Currently, the church houses the relics of Saint Nicholas of Myra, transferred from the Italian city of Bari, Saint Nikon of Pechersk, a hermit and chronicler who lived on the lands of Tamani, and Saint Ignaty Bryanchaninov. In the altar, there is a 250-year-old icon depicting Jesus Christ, gifted to the Cossacks, according to legends, by Catherine II. The icon of Blessed Xenia of St. Petersburg has been myrrh-streaming in this church since August 20, 2005. The Church of the Intercession of the Holy Virgin is the oldest in Kuban and is especially revered by the Cossacks and Orthodox residents of the region.