The tent-like church was built over the burial site of the second founder of the Ferapontov Monastery, the venerable Martynian, at the southern wall of the Nativity of the Virgin Cathedral. An inscription carved on the white stone foundation board states that the construction was completed on August 1, 1641. The construction of the church in honor of the venerable abbot Martynian began in 1640 during the reign of Tsar Mikhail Fyodorovich, Tsarevich Alexei Mikhailovich, Metropolitan Varlaam of Rostov, Abbot Gerasim, and the builder Elder Mitrophan. The completion of the construction is dated to August 1, 1641.

The church was built by masters from Kirillov. Its architecture is simple and expressive: a small cube with an octagonal tent and a thin drum. The unique lighting solution of the interior lies in the fact that the windows, located only at the top, direct sunlight onto Martynian's burial site, creating an effect of illumination. The unlit space of the tent, ending with the light drum, resembles a tunnel leading to the Heavenly Kingdom.

In 1502, on the outer southern wall of the Nativity of the Virgin Cathedral, the icon painter Dionysius depicted the Virgin of the Caves with archangels Michael and Gabriel, Saint Nicholas, and the founders of the monastery, Ferapont and Martynian, bowing at the feet of the Virgin. After the stone church of Martynian was built, this part of the fresco ended up in the arched opening of the northern wall of the church. Here, a rare depiction of the founders of the monastery has been preserved, who were not yet canonized in the early 16th century and were only recognized as saints in the middle of that century.

Since 1838, the church has housed a two-tiered iconostasis created by the Vologda merchant Nikolai Milavin. The carved royal gates have lost the figures of the archangel Gabriel and Mary from the Annunciation scene. The inscription 'Immortal Table' symbolizes the sacrament of the transformation of bread and wine into the Holy Gifts, the Body and Blood of Christ.