The origin of large subsidence in intracratonic basins is still under debate. We propose a new and self-consistent model for the formation of those basins, where lithospheric shortening/buckling triggers metamorphism and densification of crustal mafic heterogeneities. We use a forward thermo-mechanical finite element technique to evaluate this mechanism for the typical example of the East Barents Sea basin (EBB) where a very large and compensated subsidence, accommodating an up to 20-km-thick sediment succession, is observed. The lower crust in the dynamic model is modelled with petrologic-consistent densities for a wet mafic gabbroic composition that depend on pressure and temperature taking into account dehydration at high PT conditions. The model successfully explains the main characteristics of the EBB, notably the large anomalous and fast subsidence during the Late Permian–Early Triassic, its present-day geometry and the absence of a significant gravity anomaly.