The greenhouse gas (GHG) balance of boreal peatlands in permafrost regions will be affected by climate change through disturbances such as permafrost thaw and wildfire. Although the future GHG balance of boreal peatlands including ponds is dominated by the exchange of both carbon dioxide (CO2) and methane (CH4), disturbance impacts on fluxes of the potent GHG nitrous oxide (N2O) could contribute to shifts in the net radiative balance. Here, we measured monthly (April to October) fluxes of N2O, CH4, and CO2 from three sites located across the sporadic and discontinuous permafrost zones of western Canada. Undisturbed permafrost peat plateaus acted as N2O sinks (−0.025 mg N2O m−2 d−1), but N2O uptake was lower from burned plateaus (−0.003 mg N2O m−2 d−1) and higher following permafrost thaw in the thermokarst bogs (−0.054 mg N2O m−2 d−1). The thermokarst bogs had below-ambient N2O soil gas concentrations, suggesting that denitrification consumed atmospheric N2O during reduction to dinitrogen. Atmospheric uptake of N2O in peat plateaus and thermokarst bogs increased with soil temperature and soil moisture, suggesting sensitivity of N2O consumption to further climate change. Four of five peatland ponds acted as N2O sinks (−0.018 mg N2O m−2 d−1), with no influence of thermokarst expansion. One pond with high nitrate concentrations had high N2O emissions (0.30 mg N2O m−2 d−1). Overall, our study suggests that the future net radiative balance of boreal peatlands will be dominated by impacts of wildfire and permafrost thaw on CH4 and CO2 fluxes, while the influence from N2O is minor.