The Church of Archangel Michael above the Holy Gates was built around 1670. Sources link its construction to the serf Pavel Sidorovich Potehin, who initially belonged to the Shereteyevs, then to the Odoevskys, and later to the Cherkasskys. He also created architectural masterpieces such as the Church of Archangel Michael in Arkhangelsk, the Church of Nicholas the Wonderworker in Nikolsk-Uryupin, and the Church of the Life-Giving Trinity in Ostankino. All these temples, including the Church of Archangel Michael, were built according to his own designs. At the end of the 17th century, the church looked different than it does now, as seen in the icon of St. Macarius, painted by the famous iconographer Simon Ushakov in 1661. In it, the gate church is depicted with one dome and kokoshniks that taper from the upper edge of the walls to the drum of the dome. Later, the kokoshniks were hidden under the roof, and four small domes were added at the corners. These changes are captured in an image of the monastery created by A. G. Ukhtomsky in 1816.

Now, the gate church of the Makaryev-Zheltovodsky monastery appears five-domed to visitors. Inside, it is bright and modestly decorated: the walls are whitewashed, and the small iconostasis shines with whiteness and gilding. Here is an image of St. Macarius by Simon Ushakov, placed in a special kiot. During the Soviet years, the church was on the brink of destruction, as institutions that did not care for the preservation of historical buildings were located on the monastery grounds. The church and some towers miraculously did not collapse, likely due to restoration work carried out shortly before the revolution, which allowed them to last longer.

In 1948, a severe flood damaged the stone slope built in the 1880s-1890s, necessitating urgent measures to preserve the architectural and historical monument. Restoration work began then, but due to insufficient funding and the construction of the Cheboksary Hydroelectric Power Station in the late 1960s, the restoration of the walls and churches of the monastery was hindered.

Partial restoration of the gate church of Archangel Michael was carried out in 1959. The brickwork of the walls, cornices, and architraves of the drums and vaults were restored; a metal covering was also laid on the apse, transitional gallery, and vault of the main volume, which were destroyed by a fire in 1945. The final restoration of the church took place in the 1980s, and the complete restoration of the monastery buildings and fortifications began only after the transfer of the Trinity Makaryev Zheltovodsky Monastery to the Church.