This study shows that microgravity investigation can be a successful strategy to detect deep buried foundation in an urban context. Specifically, we focused on the challenging archaeological and engineering case of the “Basilica dello Spirito Santo” in Naples (Italy) where the foundation system was debated in last centuries due to its complex historical development. Here we show that microgravity data, processed through the Depth from Extreme Points (DEXP) transformation, inferred a quadrangular pattern consistent with the expected foundation reinforcements. Modelling indicates that the structure is located at ∼5 m depth, shallower than originally designed. Further geophysical investigations employing Ground Penetration Radar (GPR) reveal numerous shallow voids, interpreted as crypts and burial sites, although they did not yield conclusive evidence regarding the foundation structures. This would be likely due to weak permittivity contrasts with surrounding soils. Moreover, the data suggest the presence of a deeper elongated anomaly of uncertain origin, which could represent either a geological channel-like feature or an undocumented structure. The study demonstrates the effectiveness of multimethodological approaches in complex urban archaeological contexts, providing crucial information for both cultural heritage knowledge and restoration planning.