The UNESCO World Heritage Hadrian’s Villa lies over the Colli Albani volcanic district near Rome. Magnetic, paleomagnetic, radar, and electric resistivity surveys were performed in the Plutonium–Inferi sector to detect buried buildings and outline a segment of the underground system of tunnels that link different zones of the villa. In particular, a paleomagnetic analysis of the bedrock unit allowed to accomplish an accurate geomagnetic field modelling and characterize the archaeological sources of the magnetic field anomalies. We used a computer-assisted forward modelling procedure to generate a structural model of the sources of the observed anomalies. The intrinsic ambiguity of the magnetic field modelling was reduced with the support of ground penetrating radar amplitude slices and an analysis of radar and electric resistivity profiles. The bedrock lithology in this area is an ignimbrite tuff characterized by abundant iron oxides. The high-amplitude magnetic anomalies observed in the Plutonium–Inferi area are due to strong bedrock remnant magnetization and susceptibility contrasts between topsoil infill of cavities and the surrounding tuff. The resulting magnetization model of the Plutonium–Inferi complex shows that the observed anomalies are mostly due to the presence of tunnels, skylights and a system of ditches excavated in the tuff.