The deformation history of the Eastern Cordillera (EC) and Sub-Andean Zone (SAZ) of southern Peru is critical for understanding the roles that tectonics and climate played in the erosional exhumation of bedrock and the associated sediment flux delivered to the Amazon drainage basin. In this study, we report new field and subsurface data, apatite fission track (AFT) and (U–Th)/He thermochronological ages, U–Pb ages on detrital zircon grains, Sr–Nd isotopic compositions of fine sediments, which combined with previously published data, provide new constraints on the Neogene deformation and deposition history across the southern Peruvian EC and SAZ between 12° and 14°S. Late Miocene-Pliocene deformation is recorded by AFT and AHe ages in both the EC and SAZ and by growth strata geometry in the SAZ. This period is characterized by the development of piggy-back synclines and duplexes in the SAZ, overthrusting of the EC, and input of recycled sedimentary rocks of the SAZ and first cycle sediments from Triassic Plutonic rocks from the EC to the late Miocene-Pleistocene piggy-back syncline sediments. We report a transition from low-energy sand-dominated to high-energy conglomerate-dominated deposits in the Plio-Pleistocene marking an increase in sedimentation rates, indicating that the thrust wedge has continued to propagate. Our data agrees with that of previously published studies and indicate that the Late Miocene-Pliocene was a period of tectonic uplift and deformation in both the EC and SAZ.