Organic carbon (OC) stored in permafrost affected soils of the higher northern latitudes is known to be highly vulnerable to ongoing climatic change. Although the ways to quantify soil OC and to study connected C dynamics from ecosystem to global scale in the Arctic has improved substantially over the last years, the basic mechanisms of OC sequestration are still not well understood. Here we demonstrate a first approach to directly study micro scale soil structures mainly responsible for soil OC (SOC) stabilization using nano scale secondary ion mass spectrometry (NanoSIMS). A cross section from a permafrost layer of a Cryosol from Northern Alaska was analysed using a cascade of imaging techniques from reflectance light microscopy (RLM) to scanning electron microscopy (SEM) to NanoSIMS. This allowed for the direct evaluation of micro scale soil structures known to be hot spots for microbial activity and SOC stabilization in temperate soils. The imaging techniques were supported by classical soil analyses. Using this unique set of techniques we are able to evidence the formation of micro-aggregate structures in the vicinity of plant residues in permafrost soils. This clearly indicates biogeochemical interfaces at plant surfaces as important spheres for the formation of more complex soil structures in permafrost soils. Organo-mineral associations from these hot spots of microbial activity were recovered from plant residues (free particulate organic matter, fPOM) as fine grained mineral fraction with a typically low C/N ratio. This nicely illustrates the link between classical bulk analysis and state of the art spectromicroscopic techniques.