The existence of the church in honor of Archangel Michael in Astrakhan has been known since the mid-17th century. In documents from 1672, related to the murder of Astrakhan Metropolitan Joseph, there is mention of the 'wooden floor of the priest of the Church of Archangel Michael.' The church was located in the Zemlyanoy town, in one of the streltsy settlements along the southern wall of the White City. This settlement, known as Zmievaya, named after the streltsy colonel, was the easternmost and adjoined the wall of the Zemlyanoy town, where the Archangel Gates were located. By the end of the 17th century, Armenians began to settle near the Zmievaya settlement, for whom a stone inn was built. After the streltsy uprising of 1705-1706, most of the yards in Zmievaya settlement became deserted, and the Armenians soon fully populated it. From the early 18th century, mentions of the wooden Church of Archangel Michael at this site disappear. Its further history is connected with the Yamgurcha settlement, named after the last Astrakhan khan Yamgurcha or an influential Nogai murza.

The Russian settlement across the Kutum River appeared in the early 18th century. Colonel Mikhail Lebedev built a regimental hospital here, which housed a wooden church in honor of the icon of the Mother of God 'Joy of All Who Sorrow.' In 1727, the church burned down. By the mid-century, the Yamgurcha settlement became populous. It housed barracks for soldiers of the Caucasian linear battalion, and later a Cossack regiment. The settlement turned into a military one, but a significant urban population also lived here, engaged in crafts. The residents began discussing the construction of their own church and turned their attention to the old Resurrection Church.

The Resurrection Church was built in the Kazan streltsy settlement in the mid-17th century. The first mentions of it date back to 1672. The Kazan settlement likely appeared in Astrakhan earlier when the streltsy settled in the Zemlyanoy town. After the uprising of Stepan Razin, a soldier's regiment was sent here. By the end of the 17th century, the number of soldiers in Astrakhan increased, and they continued to settle in the Kazan settlement, later new soldier settlements appeared. In 1697, a church in honor of the Protection of the Mother of God is mentioned in the Kazan settlement, likely an altar. In 1747, the Resurrection Church had an altar in honor of the Protection of the Mother of God. The 'Klyuchariev Chronicle' states that in 1722, Governor Artemy Petrovich Volynsky, awaiting the arrival of Peter I, ordered the wooden houses in the Kremlin to be demolished and the churches to be relocated. The Resurrection Church was moved and renamed in honor of the Kazan icon of the Mother of God, which is why the settlement became known as Kazan. It is possible that the Kremlin's Resurrection Church was relocated to the site of the former local Resurrection Church, which may have burned down due to frequent fires in Astrakhan. However, the renaming of the Resurrection Church to Kazan is likely incorrect, as the settlement could have been named Kazan in honor of the regiment from Kazan.

The temple was adorned with sacred images in 1836. In 1905, new walls of the temple were painted, and the old painting was updated. The main iconostasis, made by master Fyodor Konovich Moiseev in 1901, was three-tiered, elegantly carved, and gilded on the poliment. The iconostases of the altar chapels, also gilded on the poliment, were installed in 1905. This temple was the only one in Astrakhan with sculptural representations of saints.

In 1923, the Church of Archangel Michael was seized by Renovationists. In 1936, it was closed and subsequently blown up.