The Church of Peter and Paul was previously known as the Hospital Church in the name of Macarius of Yellow Waters. In Ancient Rus, monasteries served as shelters for the elderly and sick, having hospital cells with a church on their territory. In the early 17th century, the Pechersky Monastery had wooden cells and a temple.

After the construction of a stone refectory and the freeing of the Ascension Cathedral from adjacent chapels, two of which were moved to the hospital church, the abbot Archimandrite Stefan informed Patriarch Joasaph about the dilapidation of the wooden hospital and the availability of stone materials for its construction.

On March 12, 1652, Patriarch Joasaph issued a decree to Archimandrite Stefan for the construction of a new hospital church. However, for unknown reasons, the church was built only 35 years later, in 1687, under Archimandrite Joasaph, and again from wood, consecrating it in honor of Saint Macarius of Yellow Waters and the Unzhen Miracle Worker.

By the 18th century, the temple had fallen into disrepair, and in 1738, a collection of donations for its stone construction began. Archimandrites Philaret and Jonah, the abbots of the Pechersky and Makaryevsky monasteries, donated 100 rubles each, while the treasurer of the Pechersky monastery, Filagriy, added 65 rubles.

In the same 1738, a new stone hospital church was built, "cold, single-domed, in the shape of a rectangle, six fathoms long and nine vershoks, four fathoms wide, with a stone dome, connected to the east with the brotherly and hospital cells." In 1858, under Bishop Jeremiah Solovyov of Nizhny Novgorod and Arzamas, the altar in the church was reconsecrated in honor of the holy apostles Peter and Paul.