Measurements of the land‐atmosphere exchange of the greenhouse gases methane (CH4) and carbon dioxide (CO2) in high Arctic tundra ecosystems are particularly difficult in the cold season, resulting in large uncertainty on flux magnitudes and their controlling factors during this long, frozen period. We conducted snowpack measurements of these gases at permafrost‐underlain wetland sites in Zackenberg Valley (NE Greenland, 74°N) and Adventdalen Valley (Svalbard, 78°N), both of which also feature automatic closed chamber flux measurements during the snow‐free period. At Zackenberg, cold season emissions were 1 to 2 orders of magnitude lower than growing season fluxes. Perennially, CH4 fluxes resembled the same spatial pattern, which was largely attributed to differences in soil wetness controlling substrate accumulation and microbial activity. We found no significant gas sinks or sources inside the snowpack but detected a pulse in the δ13C‐CH4 stable isotopic signature of the soil's CH4 source during snowmelt, which suggests the release of a CH4 reservoir that was strongly affected by methanotrophic microorganisms. In the polygonal tundra of Adventdalen, the snowpack featured several ice layers, which suppressed the expected gas emissions to the atmosphere, and conversely lead to snowpack gas accumulations of up to 86 ppm CH4 and 3800 ppm CO2 by late winter. CH4 to CO2 ratios indicated distinctly different source characteristics in the rampart of ice‐wedge polygons compared to elsewhere on the measured transect, possibly due to geomorphological soil cracks. Collectively, these findings suggest important ties between growing season and cold season greenhouse gas emissions from high Arctic tundra.