Lusi is a sediment-hosted geothermal system relentlessly erupting since May 2006 in the East Java back-arc sedimentary basin. Lusi provides the unprecedented opportunity to study the development of the early phases of a new-born piercement structure and its impact on society. In order to investigate the shallow plumbing system of this large-scale eruption, we deployed a pool of 25 IRIS V-Fullwavers to conduct a 3D deep electrical resistivity tomography extending over ∼15 km² around the eruption site. The inverted data reveal the structure of the subsided area hosting the region where a mix of groundwater, mud breccia, hydrocarbons and boiling hydrothermal fluids are stored. Our investigation also points out the link between a well-developed fault system and the upwelling of the deep-seated fluids that initiated, and still drive, the development of the new-born Lusi eruption.