Assessing the thermal evolution of sedimentary basins over time is a major aspect of modern integrated basin analysis. While the behavior of clay minerals and organic matter with increasing burial is well documented in different geological and thermal settings, these methods are often limited by the temperature ranges over which they can be precisely applied and by the available material. Here, we explore the emergent Δ47 clumped isotope geospeedometry (based on the diffusional redistribution of carbon and oxygen isotopes in the carbonate lattice at elevated temperatures) to refine time‐temperature paths of carbonate rocks during their burial evolution. This study provides a reconstruction of the thermal and exhumation history of the Upper Cretaceous thrust belt series in the western subalpine massifs (Bauges and Bornes, French Alps) by a new approach combining for the first time available data from three independent geothermometers. The investigated area presents two zones affected by contrasting thermal histories. The most external zone has undergone a relatively mild thermal history (T < 70°C) and does not record any significant clay mineral diagenetic transformation. By contrast, the internal zone has experienced tectonic burial (prealpine nappes) in response to thrusting, resulting in overheating (T > 160–180°C) that induced widespread clay mineral diagenetic transformations (progressive illitization from R0 to R1 and R3 illite‐smectite mixed‐layers), organic matter maturation (oil window) and Δ47 thermal resetting with apparent equilibrium temperatures above 160°C. The three employed geothermal indicators conjointly reveal that the investigated Upper Cretaceous rocks have suffered a wide range of burial temperatures since their deposition, with a thermal maximum locally up to 160–180°C. High temperatures are associated with the tectonic emplacement of up to 4 km of prealpine nappes in the northern part of the studied area. Finally, a forward thermal modeling using Δ47, vitrinite reflectance and clay mineral data, is attempted to precisely refine the burial and exhumation histories of this area.