The cave church, which includes two chapels, is a unified complex of three temples: the Clement Temple, consecrated in 1852, the Martin the Confessor Temple, consecrated in 1867, and the Andrew the First-Called Temple, consecrated in 1900. Restoration work was carried out under the guidance of architect D. M. Strukov. During the Crimean War, the church suffered significant damage. In the 1930s, it was transferred to the Sevastopol Museum and reopened in the 1990s.

Since 1991, after the Soviet period, thanks to the efforts of the abbot Archimandrite Augustine (Polovetsky, †1996), the gradual revival of the monastery began: the temples and monastic cells were restored. A particle of the honorable head of St. Clement the Holy Martyr was transferred from Kyiv, and a reliquary with his relics was established in the Holy-Clement Temple.

On January 26, 2019, weekly services were resumed in the cave temple complex, in the Church of Clement of Rome.