Excavations were undertaken in the presbytery during work to lay a new floor and identified the latest building phases of the church. The structure, built in the 11th century as the oratory to the parish church of S. Michele, was mentioned in connection with a pastoral visit in 1585. The church, with central nave and two lateral aisles, is severely out of axis in the presbytery area, evidence of the complexity of its construction history. The perimeter walls are buttressed and have ogival windows above which a brick dentil cornice runs the length of the wall. An inscribed Roman votive altar is preserved inside the church. This came from the church of San Giovanni where it had been used as the base for a holy water stoup.

The terminus post quem for the earliest identified phase is a coin from the second half of the 15th-16th century. This phase was attested by a floor with a beaten clay make up on which tiles had been laid in a herringbone pattern (of which only the impressions remain), a wall on a north-south alignment that probably divided the presbytery and a quadrangular structure situated west of the modern altar, interpreted as a pedestal/base.
A subsequent phase was attested by a second floor whose thin beaten mortar make up was only preserved in the south-western part of the apse, on a higher level than the nave and aisles. It is possible that this is the layout of the church as described in 1742, when the whitewashing of the interior and laying of a tile floor are recorded. The latter was substituted in 1834, in the presbytery, with a floor of marble slabs. Two ossuaries, built with brick depressed vaults and quadrangular trapdoors, were discovered to the sides of the modern altar.

The final identified phase related to the work undertaken when two semi-columns were built up against the inner sides of the pillars supporting the presbytery arch.