This work aims to understand the tectonic framework that influenced and controlled the karstification processes along a shallow water carbonate sequence. Both multi-scale and multi-disciplinary approaches are presented in this work to unveil the interaction between the structural network and the karstification events. In this manner, seismic, satellite, drone, Ground Penetration Radar (GPR), and field analyses were performed. The analysis of 3D seismic data highlighted the presence of a Cretaceous NW-SE striking kilometric scale fault zone (Poço Verde Fault System) characterized by a negative-flower structure associated with a transtension fault composed of synthetic and antithetical faults. A seismic profile localized along the fault tip portion of the Poço Verde Fault System confirms this fault architecture. After analyzing regional lineaments in Shuttle Radar Topography Mission (SRTM) data and high-resolution drone images, we have identified two main fault sets localized along the Poço Verde fault tip zone. Here, a main NW-SE striking fault set and a minor N-S striking fault set are present. These structural features are associated with different tectonic phases. In this sector, the Furna Feia Cave System is localized. Furthermore, field evidence indicates a Cenozoic reactivation of pre-existing structures, which has led to an increase in fracture density and intensity. A dolomitic interval in GPR sections appears more deformed compared to the limestone portions. The presented work suggested that the Poço Verde Fault impacted, controlled, and promoted both dolomitization and karstification processes that affected the studied carbonate rocks.