Following a geophysical survey the excavations at Faragola began in 2003.
Previously, the first occupation of the site had been dated to the Daunian period, as attested by a cobble mosaic. However, the discovery in 2006 of a semi-chamber tomb, which had been converted into a tank during late antique restructuring, shed light on the organization of the pre-Roman Daunian village (datable to at least the 4th-3rd century B.C.) and in general on the phases preceding the villa, before the Roman conquest of Daunia. There is limited data for the late Republican and early-middle Imperial periods, to which the first phase of the villa at Faragola dates. This first phase was attested by several structures in opus incertum, later reused as foundations for the walls of the late antique phase, an oscillum and a marble statue of a boy hunter, resembling Eros, in one of the rooms of the late antique bath complex (2nd century A.D.).

The 2006 campaign provided new data regarding the complex architecture and functioning of the villa, highlighting the central role of the baths beside the coenatio, which were linked to the latter by a long corridor. The excavations uncovered the natatio, an integral part of the frigidarium, a sudatio and a second bath complex, of smaller size standing next to, but separate from the first and with a separate entrance, warm and hot rooms and a preafurnium. The second set of baths was probably used by those who worked at the villa, whilst the larger and better organized complex may be interpreted as that belonging to the owners, that is for the use of the dominus and his family. Two sets of baths in a private rural residence are however rare. A large room, partially covered by a mezzanine floor was also investigated. This may have been used for the preservation of foodstuffs and a storeroom as suggested by a series of metal artifacts and pottery vessels found along the walls (where there were once perhaps wooden shelves), a latrine, with relative system for water provision and waste disposal, and two square features, perhaps light wells.

The finds relating to the medieval village (7th-8th century B.C.) which developed in the area of the villa following its abandonment, confirm that the form acquired by the villa in the 5th century A.D. did not last long. In the late 6th century what had been the coenatio was used as a stable and/or rubbish dump, whilst the other rooms housed craft activities for the production of bronze and lead (as attested by several smelting pits, work surfaces and metal waste products). The phases regarding the baths and the storage areas were more complex. Between the walls of the late antique villa, which were still preserved, huts were constructed, in part resting on the pre-existing walls, in part resting on posts which held up the beams. In the case of the large rectangular storage rooms the old walls were used as an enclosure housing huts which perhaps had wooden silos for grain storage. Other spaces were used for burial purposes, as documented by the infant graves.