Burials traceable to eleven individuals were found along the northern side of the church. Mostly arranged as best as possible directly following the profile of the rock bank and hence oriented in different directions; the presence of nails suggests that some of the buried were placed in wooden boxes. Few items of funerary equipment were found, such as bone pins, hollow bronze cylinders and a ring of the same metal. Only two burials have been hypothesised to have been carried out in a phase prior to the construction of the church, while the rest of them certainly occurred after its construction.

Among the archaeological evidence that has emerged, outside, along the western side, there is a burial excavated in the rock bank, traceable to an individual of the 6th century BC, with a single piece of equipment, a trefoil jug. A copper coin, datable to the 15th century and reused as a pendant, was found near the excavation area in the 1990s.

In the southern courtyard of the monastery, in the cloister, excavations have brought to light an elaborate and widespread canalisation system and wells dug in the rock bank; in general similar remains have emerged in different points of the architectural complex. They were used for agricultural activities prior to the installation of the medieval buildings and are specifically connected to the cultivation of vines. Similar testimonies, which can be dated between the Greek age and the Roman Republican age (6th century BC), are quite widespread in the surrounding area, such as those that emerged at Torre Montello, in the locality of Le Petrose and during the excavations at the Eni refinery.

Archaeological investigations inside the refectory, which was probably built in the 14th century, have brought to light two barrel-vaulted cisterns, of different sizes, datable to the building’s installation phase.
At the north-western corner of the structure, a short distance from the larger cistern, the remains of a pavement delimited by two partially preserved wall structures have been identified; these remains belong to a room in which it is possible to assume that there was a kitchen which was used starting from the 15th-16th century.

On the basis of some structural elements, one can assume that the recovered portion of the boat probably belongs to the stern. The archaeological excavation and archaeometric carbon-14 dating  have made it possible to date it between the 16th and 17th centuries AD The investigation has also made it possible to recover numerous archaeological finds which, due to the poor conditions in which they were found, do not allow to identify the possible elements regarding the cargo of the only known wreck in the bay, or to isolate ceramic groups referable to cargoes of other boats or to the frequentation of the islet of San Nicolicchio in ancient times. These, in fact, can be dated from the 4th century BC to the present day.

Several evidence of anthropic presence has been discovered here over the years. Indeed, traces belonging to the Neolithic age and sporadic evidence of the Imperial Roman age (2nd-3rd century AD) have emerged. There are writings on quarry cuts, post holes and some burials probably dating back to the Middle Ages are documented.
From the sources we learn that the monastery of San Nicola Vetrianolo was present on the islet, donated in 1119, together with Santa Maria della Giustizia, to the church of San Pietro Imperiale (now San Domenico in the Old Town). The document mentions the presence of two small fishing boats, used by the monastery.
Later on, the islet of San Nicolicchio had a strategic function and was a landing place for Spanish and French troops, who set up a defensive battery with six cannons at the beginning of the 19th century.