The crypt, entirely carved into the tuff rocks, is the result of modifications and additions in the place and in the architecture, as demonstrated by the two circular columns with Doric capital of the sixteenth century, the addition of an altar on the east wall, topped by a seventeenth-century fresco depicting the Crucifixion (hence the name of the crypt), a skylight created later and the occlusion of the original entrance on the west. It is accessible through the northern door, which is followed by a barrel-vaulted staircase that leads to the underground room. The entrance is decorated with a frescoed lunette with the Holy Family scene. Inside, the walls and ceiling are covered with frescoes dating between the thirteenth and the seventeenth century, accompanied by inscriptions in Greek and in Latin. The oldest painting cycle (XIII century) includes the 'Annunciation, the Christ Pantocrator, the Virgin of Tenderness, the enthroned Mary and St. Nicholas from the early fourteenth century. Painted on the ceiling are Crusaders’ shields alternating with shields with black cross, symbol of the Teutonic Knights, and shields with the red cross, the symbol of the Templar Knights. Also painted on the ceilings are stars, plant motifs and real and imaginary animals, such as the large Hydra, a figure from Greek mythology.