The church in honor of St. Macarius of Yellow Water is located north of the Trinity Cathedral, on the site of the former chapel of the cathedral, consecrated in his name. Its construction took place in 1808-1809, during a time when the monastery was still thriving. At that time, few could have predicted that less than ten years later, with the relocation of the fair from Makaryev to Nizhny Novgorod, the monastery would begin to decline.

The Makaryev church was envisioned for a long and prosperous future. It is designed in the classical style with elements of 'metropolitan' elegance. Special attention is drawn to the colonnade of the Tuscan order, connecting the church with the Trinity Cathedral. The facades of the church on the western and northern sides are adorned with four-column porticos, and the main volume is topped with a wide drum and a powerful dome. In the late 1920s, the church was closed by the new authorities, shortly after the monastery was closed in 1927. From August 1943 to November 23, 1988, the building was rented by the Lyskov Veterinary Technical School.

Only in 1992 was the church building, like other churches of the monastery, transferred to the Russian Orthodox Church. The restoration and revival of the frescoes in 2005-2006 were carried out by Vladimir Ivanovich Nekrasov, a painter and iconographer from Vladimir. In early August 2008, the President of the Russian Federation, Dmitry Medvedev, visited the Makaryev Yellow Water Women's Monastery. During the visit, he toured the monastery, visited the Makaryev church and the Trinity Cathedral, and venerated the relics of St. Macarius of Yellow Water and Unzhen.