During the preparatory phase of the Pauline Year, celebrated between 2008 and 2009, while excavation work was underway to create some services for the reception of pilgrims in the southwestern area, adjacent to the Abbey's garden, a series of archaeological remains dating back to the early Middle Ages were unearthed. The overlying modern construction was completed, but a "zone of protection and safeguarding" was created underground for these unique remains, which were only mentioned in an inscription preserved at the Abbey dating back to the time of Pope Gregory the Great (590-604).

This inscription refers to a female community of a monastery with an oratory dedicated to Saint Stephen. The remains of a portico, columns, a well, and a bell tower have emerged. Further archaeological investigations were conducted by the Vatican Museums and the Pontifical Institute of Christian Archaeology, which, thanks to the financial support of the Patrons of the Arts in the Vatican Museums, carried out a restoration and museum arrangement project open to the public, creating a tour path of the excavation area. The project also saw the participation of the School of Specialization in Architectural Heritage and Landscape of the "Sapienza" University of Rome.