Archaeological excavations began in 2003, thanks to a research and enhancement project promoted by the Cavaion Municipality and directed by the then Veneto Archaeological Heritage Superintendency, with the support of the Region. They brought to light, on the summit of Mount San Michele, a settlement built in the Middle Ages, surrounded by fortification structures and spread over several terraces. On the highest terrace, buildings with traces of hearths and earthen floors were brought to light. The considerable size of some of the rooms, supported at the centre by one or two pillars, suggests the stable presence of a military garrison linked to the war events that took place in this area, during the war of Venice and Mantua against the Da Carrara family (1404) and the subsequent war of the League of Cambrai. In the area below the summit of the hill, the church of San Michele, destined for the care of souls of the people of Cavaion and Incaffi, has stood since at least the 11th century. All around the church, a cemetery area developed from its foundation, documented by several burials of adults and children in the bare earth, the presence of which is also recorded in some 15th-century wills and in the records of pastoral visits. Investigations distinguish five construction phases of the church complex between the end of the 11th and the 15th century.

PHASE I (late 11th century): construction of the first ecclesiastical building, characterised by an apse and a 9-metre-long nave.

PHASE II (late 12th century): the original west-facing façade wall was demolished and the nave lengthened to 13.60 meters. In the course of the two Romanesque construction sites, two furnaces for casting bronze bells were built inside the church.

PHASE III (13th century): the church was enlarged towards the north and a second apsidal nave was built. This phase can be placed in this century thanks to significant coin finds.

PHASE IV (14th century): a residential complex was built on the north side of the church, for the use of the hermit keepers, with small rooms surrounding a large rectangular area, partly built on, partly courtyard and partly occupied by a cemetery.

PHASE V (15th century): the entire residential complex was reorganised around the central courtyard, which was equipped with a Venetian-style well.

Acts of pastoral visits, between the 16th and 18th centuries, continue to attest to the church's attendance, albeit sporadic, after the parish church of St John the Baptist had been recognised as a parish since the 14th century. Severely damaged by French soldiers at the beginning of the 18th century, the church was later reconstructed, but subsequently suffered such degradation that by 1807, when it was taken over by the Royal State Property Office following the Napoleonic suppressions, it was hopelessly dilapidated and in ruins. Some of the sacred stones were later re-employed in the erection of Cavaion's new parish church in the early decades of the 19th century.