"The work of the archaeologist's pickaxe is awaited," wrote Fr. Bagatti in 1967 as he contemplated the site once occupied by el-Mejdel. The pickaxe took a little time to arrive.

In 1971, the Franciscan priests Virgilio Corbo and Stanislao Loffreda began the excavations, bringing to light the dock of the Hellenistic and Roman port of Magdala (2nd century B.C. - 2nd century A.D.), with its adjacent square flanked by four monumental porticoes. Next to this square was a complex of Roman baths, with a mosaic that depicted, among other things, a 1st-century ship. Nearby were some Jewish ritual baths (mikveh), and in this context was an elegant square building that Fr. Corbo thought was a "mini-synagogue"; although today, many doubt that it was, the small building remains a mystery. Archaeologists discovered the remains of a Byzantine monastery (5th-7th centuries A.D.) at the southern end of the site and partially outside of it, with several rooms decorated with exquisite mosaic floors. Additionally, just outside the gate of their site, the Franciscans found the remains of what might be the monastery's church. Although it lacked the typical semicircular apse, it was a three-nave building, and scattered throughout it were remains of a chancel (communion rail).