<i>Background and aims</i> Approximately 50 % of belowground organic carbon is present in the northern permafrost region and due to changes in climate there are concerns that this carbon will be rapidly released to the atmosphere. The release of carbon in arctic soils is thought to be intimately linked to the N cycle through the N cycle’s influence on microbial activity. The majority of new N input into arctic systems occurs through N₂-fixation; therefore, N₂-fixation may be the key driver of greenhouse gases from these ecosystems.<br/><i>Methods</i> At Alexandra Fjord lowland, Ellesmere Island, Canada concurrent measurements of N₂-fixation, N mineralization and nitrification rates, dissolved organic soil N (DON) and C, inorganic soil N and surface greenhouse gas fluxes (CO₂, N₂O and CH₄) were taken in two ecosystem types (Wet Sedge Meadow and Dryas Heath) over the 2009 growing season (June-August). Using Structural Equation Modelling we evaluated the hypothesis that CO₂, CH₄ and N₂O flux are linked to N₂-fixation via the N cycle.<br/><i>Results</i> The soil N cycle was linked to CO₂ flux in the Dryas Heath ecosystem via DON concentrations, but there was no link between the soil N cycle and CO₂ flux in the Wet Sedge Meadow. Methane flux was also not linked to the soil N cycle, nor surface soil temperature or moisture in either ecosystem. The soil N cycle was closely linked to N₂O emissions but via nitrification in the Wet Sedge Meadow and inorganic N in the Dryas Heath, indicating the important role of nitrification in net N₂O flux from arctic ecosystems.<br/><i>Conclusions</i> Our results should be interpreted with caution given the high variability in both the rates of the N cycling processes and greenhouse gas flux found in both ecosystems over the growing season. However, while N₂-fixation and other N cycling processes may play a more limited role in instantaneous CO₂ emissions, these processes clearly play an important role in controlling N₂O emissions.