Excavations from 1993 to 1996 by the Pontifical Institute of Medieval Studies at the University of Toronto uncovered areas around the gate house and the cloister.

Some scholars believe that the abbey had been built in the same location, or general area as an ancient Greek temple dedicated to Artemis, which is supported by the fact that materials from a temple have been extensively used in the buildings of the monastery; it is possible, however, that these elements (reused column drums, for example) came from the ancient city a few hundred metres away.

The main surviving structures are the imposing vaulted gate house and the church, especially its western end as well as parts of the defensive wall around the monastery.

Excavation to the NE of the east end of the church (possibly a narthex was originally planned but never completed) revealed an arched entrance probably to the refectory which had fallen in an earthquake.

A number of graves from this later reoccupation were excavated in and around the cloister, including a headless man and one with a German banker's token of the mid 16th century.