The Val d’Agri Basin is a Quaternary sedimentary basin topping multiple tectonic units of the southern Apennines fold-and-thrust belt and a giant oilfield within deeper Apulian Platform carbonates. This basin is bounded by the seismically active East Agri (EAFS) and Monti della Maddalena (MMFS) extensional fault systems. The reservoir rocks are sealed and separated from shallower thrust sheets by a clay-rich and overpressured mélange. The role of this mélange during fault evolution at shallow crustal levels is widely debated and perhaps underestimated. Here, through multi-scale structural analyses and U–Pb dating of syn-tectonic calcite mineralizations, we gain new insights into the Val d’Agri fault system architecture, their structural maturity, and their relations with both natural and induced seismicity. Consistent with present-day NE-SW crustal stretching, the macro-scale structural architecture of both EAFS and MMFS is controlled by NW-SE and NE-SW fault sets, which displaced and in part re-sheared inherited pre- and syn-orogenic structures. The lack of evident clustering of meso-scale faults and the radial pattern of related slickenlines suggest that polygonal-like faulting occurred, particularly along the EAFS, due to lateral spreading of the Irpinia mélange in the subsurface. Structural data show that the MMFS is characterized by a higher structural maturity (slip longevity), with calcite U–Pb ages indicating the onset of long-lasting extensional tectonics in Early-Middle Miocene time. The original results are discussed in terms of seismotectonic setting of the study area, emphasizing the role played by both the thickness and spatial distribution of plastic mélange in modulating fluid pressure and seismic faulting.