When the original refectory was transformed into a mosque in the 11th century, a new refectory was built, to the east of the basilica, adjoining the ancient kitchen area in the northeast corner of the monastery. The arches of this structure were constructed from limestone blocks, and the lower reaches are covered with coats of arms and inscriptions in Latin, French, and German, the record of pilgrims who came from the West during the time of the Crusades and in the centuries subsequent to that time. Quite a number of these have been identified by modern scholars.

On the eastern wall are thirteenth century depictions of the Prophet Elias being fed by a raven, and of Saints Anthony and Paul breaking bread that had been supplied by an angel. In the apse is a depiction of the Hospitality of Abraham, painted in 1577, and above, a fresco of the Second Coming of Christ, painted in 1573. This is often depicted in monastery refectories, to remind the monks of the transience of this life, and the need to prepare for the life to come, which is eternal. The room is dominated by an immense walnut table decorated with elaborate carving. This seems to be a table of the fifteenth century, that was sent to the monastery from the island of Zakynthos in the eighteenth century. The eleventh century refectory has recently been restored, and is again in daily use by members of the community. It was dedicated on the feast of Saint Catherine in the year 2004.