Electric resistivity surveys in karst environments are commonly employed to establish parameters that can help in the evaluation of collapse risk related to sinkhole or cave formation. However, these surveys are often executed from the surface with consequent limits in resolution and identification potential as a function of coverage thicknesses. Application of these methodologies directly inside known caves, for a better understanding of their formation mechanisms, is uncommon due to accessibility problems, the nontrivial referencing issues that arise when operating in an underground environment and the challenging 2D/3D interpretation issues emerging from the presence of the cavity itself. This paper reports on the application of electric resistivity tomography along with specific geological and topographic mapping, inside the Borna Maggiore di Pugnetto karst collapse cave. Comprehensive knowledge of this cave, developed in mica‐rich and carbonate‐rich calcschists, is problematic with traditional investigations, due to the cave breakdown that masks its structure. In this study, the 3D geometry of the cave is reconstructed using a topographical survey. This reconstruction is then utilised to perform a 3D inversion of the electrical resistivity tomography (ERT) dataset. The results of both 2D and 3D inversions are compared and discussed, focusing on the survey's ability to identify resistivity anomalies within the 3D volume surrounding the cave. Additionally, an open‐source script is provided to facilitate the replication of this 3D modelling and inversion in similar underground contexts. Results of the paper show the effectiveness of the proposed surveys in the delineation of genesis and actual structure of the cave. The paper also proposes a methodological approach that can be adopted in similar contexts to enhance the understanding of speleogenesis.