Permafrost soils in the northern hemisphere are known to harbor large amounts of soil organic matter (SOM). Global climate warming endangers this stable soil organic carbon (SOC) pool by triggering permafrost thaw and deepening the active layer, while at the same time progressing soil formation. But depending, e.g., on ice content or drainage, conditions in the degraded permafrost can range from water-saturated/anoxic to dry/oxic, with concomitant shifts in SOM stabilizing mechanisms. In this field study in Interior Alaska, we investigated two sites featuring degraded permafrost, one water-saturated and the other well-drained, alongside a third site with intact permafrost. Soil aggregate- and density fractions highlighted that permafrost thaw promoted macroaggregate formation, amplified by the incorporation of particulate organic matter, in topsoils of both degradation sites, thus potentially counteracting a decrease in topsoil SOC induced by the permafrost thawing. However, the subsoils were found to store notably less SOC than the intact permafrost in all fractions of both degradation sites. Our investigations revealed up to net 75% smaller SOC storage in the upper 100 cm of degraded permafrost soils as compared to the intact one, predominantly related to the subsoils, while differences between soils of wet and dry degraded landscapes were minor. This study provides evidence that the consideration of different permafrost degradation landscapes and the employment of soil fractionation techniques is a useful combination to investigate soil development and SOM stabilization processes in this sensitive ecosystem.