Permafrost thaw will release additional carbon dioxide into the atmosphere resulting in a positive feedback to climate change. However, the mineralization dynamics of organic matter (OM) stored in permafrost-affected soils remain unclear. We used physical soil fractionation, radiocarbon measurements, incubation experiments, and a dynamic decomposition model to identify distinct vertical pattern in OM decomposability. The observed differences reflect the type of OM input to the subsoil, either by cryoturbation or otherwise, e.g. by advective water-borne transport of dissolved OM. In non-cryoturbated subsoil horizons, most OM is stabilized at mineral surfaces or by occlusion in aggregates. In contrast, pockets of OM-rich cryoturbated soil contain sufficient free particulate OM for microbial decomposition. After thaw, OM turnover is as fast as in the upper active layer. Since cryoturbated soils store ca. 450 Pg carbon, identifying differences in decomposability according to such translocation processes has large implications for the future global carbon cycle and climate, and directs further process model development.