High Arctic polar deserts cover 26% of the Arctic. Increasing temperatures are predicted to significantly alter polar desert freeze-thaw and biogeochemical cycles, with important implications for greenhouse gas emissions. However, the mechanisms underlyingthese changing cycles are still highly uncertain. Cryoturbic, carbon-rich Bhy horizons (diapirs) in frost boils are key nutrient sources for Salix arctica. We hypothesized that diapirism leads to organic carbon characteristics that alter microbial pathways, which then control root foraging and greenhouse gas production. During July–August 2013, we characterized soil properties and examined gross nitrogen transformation rates in frost boils both with and without diapirs in two High Arctic polar deserts (dolomite and granite) near Alexandra Fjord (78°51′N 75°54′W), Ellesmere Island, Nunavut, Canada. Diapiric frost boils had 18% higher soil organic carbon in the dolomitic and 9% higher in the granitic deserts, and 29% higher total dissolved nitrogen in the dolomitic desert. However, diapirs decreased gross nitrogen mineralization rates by 30% in the dolomitic and by 48% in the granitic deserts. Attenuated total reflectance Fourier transformed mid-infrared spectroscopy revealed greater concentrations of polysaccharides and recalcitrant carbon in diapiric versus non-diapiric frost boils. These increased polysaccharide concentrations likely facilitate diapirism as soil viscosity increases with polysaccharides. Lower microbial activity or ectomycorrhizae that are known to colonize S. arctica may accumulate total dissolved nitrogen in diapirs. Our results suggest geomorphologic-plant-microbe interactions may underlie important patterns of geochemical cycling in arctic systems. Thus, polar desert frost boils should represent a key focus of futre investigations of climate change in arctic systems.