We have measured the land-atmosphere CO2 exchange using the eddy covariance technique in a high Arctic tundra heath in northeast Greenland (Zackenberg). On the basis of 11 years of measurements (2000–2010), it was found that snow cover dynamics was important for the CO2 exchange. The start of CO2uptake period correlated significantly with timing of snowmelt. Furthermore, for years with deep and long-lasting snowpacks, the following springs showed increased CO2 emission rates. In the first part of the study period, there was an increase of approximately 8 g C m−2 yr−1 in both accumulated gross primary production (GPP) and CO2 sink strength during summer. However, in the last few years, there were no significant changes in GPP, whereas ecosystem respiration (Reco) increased (8.5 g C m−2 yr−1) and ecosystem CO2 sink strength weakened (−4.1 g C m−2 yr−1). It was found that temperature and temperature-related variables (maximum thaw depth and growing degree days) controlled the interannual variation in CO2 exchange. However, while Reco showed a steady increase with temperature (5.8 g C m−2 °C−1), the initial increase in GPP with temperature leveled off at the high end of observed temperature range. This suggests that future increases in temperature will weaken the ecosystem CO2 sink strength or even turn it into a CO2 source, depending on possible changes in vegetation structure and functioning as a response to a changing climate. If this trend is applicable also to other Arctic ecosystems, it will have implications for our current understanding of Arctic ecosystems dynamics.