The main aim of the second campaign inside the church of San Proto was the continuation of the stratigraphic excavation in the building’s central sector. In the apse area the 18th century altar was removed, revealing one of earlier date, in phase with the floor of terracotta tiles belonging to the sixteenth century phase. The earlier altar was a stone structure, probably built with reused material, with a hole in the top for the deposition of relics. The excavation uncovered a fourth burial at the north-western edge of the church. This was a wooden coffin placed in an earth grave with similar characteristics to the other three tombs investigated in 2009. Three of the tombs were on the same alignment but tomb 1 was in a central, privileged, position in a simple earth grave without a wooden coffin. These burials containing no grave goods but only artefacts relating to the clothing, document the cemetery use of the church in the late medieval period. The investigations showed that this was not a general practice but involved a restricted area within the church and was probably limited to certain individuals, perhaps members of a family linked to the construction of the church in the 15th century. The late medieval church had a simple rectangular plan (the apse area has yet to be fully investigated) and a very modest beaten-earth floor. The excavation showed that the church stood on the abandonment levels of the Early Christian basilica, attested by dumps of rubble (mortar, opus signinum, mosaic tesserae, stone blocks, tiles). The rubble had been used to fill the robbing trenches in the earlier structures relating to the 4th-5th century complex. No evidence of intermediate occupation was present in the stratigraphic sequence, although at the moment it cannot be excluded that the late medieval construction damaged the original stratigraphy.

One of the robber trenches was seen to relate to a wall which must have joined the wall traditionally interpreted as the northern perimeter of the “memoria di San Proto”, in phase with the mosaic floor of the same late antique building (excavated in the 1960s). This would suggest that the Early Christian complex covered a much larger area. Its occupation phases are attested by pottery datable to between the 4th-6th century A.D.