The Monastery of St Mary occupies the high ground at the centre of Apollonia and is itself one of the most attractive buildings on the site. The thirteenth-century Byzantine church at its heart is built into a later Franciscan compound; together the buildings form a quiet, well-preserved enclosure with thick stone walls and arched cloisters.
The monastery now also houses the Apollonia Museum, with sculpture, coins, and architectural fragments from the excavations. The collection is small but excellent. Visitors usually combine the church, the cloisters, and the museum in the same loop.