Hadrian’s Villa is an ancient Roman archaeological site built over an ignimbritic tuff and characterized by abundant iron oxides, strong remnant magnetization, and elevated magnetic susceptibility. These properties account for the high-amplitude magnetic anomalies observed in this site and were used as a primary tool to detect deep archaeological features consisting of air-filled and soil-filled cavities of the tuff. An integrated magnetic, paleomagnetic, radar, and electric resistivity survey was performed in the Plutonium-Inferi sector of Hadrian’s Villa to outline a segment of the underground system of tunnels that link different zones of the villa. A preliminary paleomagnetic analysis of the bedrock unit and a high-resolution topographic survey by aerial photogrammetry allowed us to perform a computer-assisted modelling of the observed magnetic anomalies, with respect to the archaeological sources. The intrinsic ambiguity of this procedure was reduced through the analysis of ground penetrating radar and electric resistivity profiles, while a comprehensive picture of the buried archaeological features was built by integration of the magnetization model with radar amplitude maps. The final subsurface 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.