The chapel, founded in the 16th century by Bishop Jonas of the Lithuanian princely family and dedicated to St. Mary Magdalene, was later known as the Bishops’ Chapel, since the crypt beneath it served as the burial place of the bishops of Vilnius Cathedral. For a long time, the Blessed Sacrament was kept in the tabernacle on this chapel’s altar, and this title therefore also became established.

On the ceiling of the chapel there is a fresco depicting Christ blessing all the worshippers, flanked by two angels. At the beginning of the 20th century, the chapel was decorated with figures of angels, Eucharistic symbols, and monograms of Jesus Christ executed in the sgraffito technique. The author of these works was Jurgis Hoppenas.

An epitaph dedicated to Bishop Antanas Pranciškus Audzevičius (1833–1895) is installed on the eastern wall. On a white marble slab, a Latin text is carved in gilded letters, with the monogram—an abbreviated form of Christ’s name—below it. Above the slab are a crossed bishop’s staff and a cross, and higher up, in a niche, stands a marble bust of the bishop. Above the altar hangs an 18th-century painting “St. Thomas” by an unknown artist.