After the closure of the Assumption and Prince Vladimir Cathedrals, the role of the main church of Astrakhan was taken over by the Intercession Cathedral, located in the northern part of the city beyond the Kutum River. In the 19th century, this area was considered a remote outskirts, where state peasants settled, forced to farm on the saline soils of the Boldin Steppe. Full development and construction of the area began only after a major fire in 1858, when the Zakutum part of the city had to be rebuilt from scratch. Many coopers, wheelwrights, and blacksmiths were relocated here. The old churches became cramped for the growing local population, and it became clear that a new large church was needed in the center of Selene, as this area was then called. The initiator of the cathedral's construction was the well-known Astrakhan merchant Ivan Ivanovich Gubin, who took on most of the expenses, amounting to almost 95 thousand rubles. In gratitude for his contribution and assistance in the church's improvement, Gubin was elected as the church elder for life.

The red brick church is designed in an eclectic style with original architecture and elusive Eastern motifs, giving it a local flavor. The large ornate dome of the light drum is now gilded, which corresponds to modern tastes, while previously it was gray and harmoniously blended with the red brick of the building. The tented spire of the bell tower, which after restoration became inexplicably blue, does not harmonize with the gilded top of the cathedral. Care should have been taken in choosing colors. These updates to the exterior were made to the Intercession Cathedral for the 450th anniversary of the city, and the reconstruction was more cosmetic in nature.

The Intercession Cathedral was luckier than many other Astrakhan churches. It was not seized by the Renovationists; here served and was buried Archbishop Philip Stavitsky, a well-known opponent of Renovationism, who did not escape imprisonment and exile during the Soviet era. The church was closed for only 9 months in 1941, during which its interior remained untouched: the frescoes, iconostasis, relics, the ancient icon of the Intercession of the Most Holy Theotokos, and the reliquary with a particle of the Honorable Tree of the Cross of the Lord were preserved. During this time, the building was used as a sugar warehouse. In 1942, prayers once again resounded in the church.