The Church of the Prophet Elijah is a small one-story building shaped like a square with a semicircular altar. It was constructed using massive bricks. Two additional rooms, which previously served as a hospital ward and a dining room with a kitchen, adjoin the church. These buildings were erected at different times, which is noticeable at the joints between them. There is a "hearing opening" between the church and the wards, covered with a metal grate, so that patients could hear and see the church services.

The northeastern part of the monastery courtyard, where the hospital wards and the Elijah Church are located, became the burial site for those who died in the battles of 1610. The legend of the existence of a cemetery at this site was confirmed between 1955 and 1960 during the construction of a water tower and the laying of water pipes. Thus, the Church of the Prophet Elijah with the hospital wards, built on the remains of ancestors, serves as a monument to the heroes who fell in battles for the Motherland.

In memory of the tragic events of 1610, when the Poles destroyed the monastery and killed all its defenders, a stone cross was erected near the Church of the Prophet Elijah. This church marked the beginning of a new history for the monastery at the end of the 20th century. In 1991, after the transfer of the Pafnutiev Monastery to the Kaluga Diocese by the Soviet authorities, the monks returned to the monastery and began conducting the first services in this church. On April 13, 1991, the consecration of the Elijah Church with the hospital wards took place, and the relics of Saint Charalampius, Bishop of Magnesia, were placed in the altar.