The catacombs were discovered in 1931 by Father Antonio Bellucci, who began the systematic excavations that brought to light the whole complex of the cemetery.

In fact, the catacombs of St Ephebes had already been discovered earlier on in the sixteenth century. The Capuchin friars of the former monastery of St Ephebes, however, had fenced off the access for fear that this spiritual place would become a centre for pilgrims and curious individuals.

The cemetery tunnels have often been altered due to the inclusions of later areas such as, for example, the introduction of considerably deep cisterns.

Since 2016, archaeological excavation and restoration was undertaken, thus, bringing to light major structures and important frescoes, including a representation of three saints, probably from the sixth century.