In the last decades, multidiscipline investigation of the Apennine mountain belt of peninsular Italy has provided fundamental insights into the genesis and evolution of wedge-top basins. In this study, we focus on shallow-water to continental, Pliocene–Quaternary basins that formed on top of the southern Apennine allochthonous wedge after its emplacement onto a large foreland carbonate platform domain (Apulian Platform). The wedge-top basins analyzed in this study are mostly asymmetric, being bounded to the north by a normal fault showing evidence of synsedimentary activity. The basin successions are generally deformed by open folds and reverse faults resulting from shortening coeval with the sedimentation of the Lower Pliocene to lower–middle Pleistocene, upper part of the basin fill. Anisotropy of magnetic susceptibility data from the basin successions are consistent with a basin evolution characterized by an initial stage of tectonic subsidence controlled by roughly north-northwest–south-southeast-oriented extension, followed by southwest–northeast shortening active during subsequent basin filling. The latter shortening is marked by a dominant northwest–southeast mean trend of the magnetic lineation obtained from most sites in the study area and is interpreted as a result of upward propagation of deep-seated deformation (tectonic inversion) taking place within the buried Apulian Platform sitting in the footwall to the allochthonous wedge. Therefore, our results emphasize a complex interplay of different tectonic processes controlling wedge-top basin development.