The currently observed climate warming will lead to substantial permafrost degradation and mobilization of formerly freeze-locked matter. Based on recent findings, we assume that there are substantial stocks of inorganic nitrogen (N) within the perennially frozen ground of arctic ecosystems. We studied eleven soil profiles down to one meter depth below surface at three different sites in arctic eastern Siberia, covering polygonal tundra and river floodplains, to assess the amount of inorganic N stores in arctic permafrost-affected soils. Furthermore, we modeled the potential thickening of the seasonally unfrozen uppermost soil (active) layer for these sites, using the CryoGrid2 permafrost model and representation concentration pathway (RCP) 4.5 and 8.5 scenarios. The first scenario, RCP4.5, is a stabilization pathway that reaches plateau atmospheric carbon concentrations early in the 21st century; the second, RCP8.5, is a business as usual emission scenario with increasing carbon emissions. The modeled increases in active layer thickness (ALT) were used to estimate potential annual N mobilization from permafrost-affected soils in the course of climate-induced active-layer deepening. We observed significant stores of inorganic ammonium in the perennially frozen ground of all investigated soils, up to 40-fold higher than in the active layer. The modeled ALT increase until 2100 under the RCP8.5 scenario was between 19 ± 3 cm and 35 ± 6 cm, depending on the location. Under the RCP4.5 scenario, the ALT remained stable in all investigated soils. Our estimated mean annual N release under the RCP8.5 scenario is between 8 ± 3 mg m−2 and 81 ± 14 mg m−2 for the different locations, which reaches values up to the order of magnitude of annual fixation of atmospheric N in arctic soils. However, the thawing induced release of N represents only a small flux in comparison with the overall ecosystem N cycling.