We used vitrinite reflectance and mixed-layered clay minerals to investigate levels of diagenesis of the Oligocene-Miocene basin developed on the nappes of the Alpine orogen exposed in the Peloritani Mountains (NE Sicily). Paleothermal indicators were integrated with stratigraphic and structural analyses and published apatite fission-track and (U-Th-Sm)/He ages to define the late evolutionary stages of the Peloritani Mountains. This multimethod approach allowed us to reconstruct the paleogeothermal gradient of the basin in Oligocene-Miocene times, to constrain its burial evolution, and discriminate between areas where it has been affected by sedimentary and/or tectonic load. In the southern area of the basin, organic and inorganic thermal parameters increase as function of depth, suggesting that their evolution was ruled by sedimentary burial. They record a decrease in paleogeothermal gradient values marking the evolution of the basin from a forearc to a thrust-top setting during the convergence-collision process between the Calabria-Peloritani Arc and the African plate. On the other hand, in the northern edge of the basin, vitrinite reflectance values (0.46%–0.58%) indicate that the thermal evolution of this area was controlled by tectonic burial related to late Langhian–early Serravallian out-of-sequence thrust tectonics. The tectonic overburden has been totally removed by extensional tectonics and/or erosion since the late Miocene. The short time span at maximum temperature (<2 m.y.) elapsing between thrust stack emplacement and the beginning of tectonic overburden removal has allowed only vitrinite reflectance and thermochronological indicators to record this compressive reactivation.