Abstract Arctic tundra is a globally important store for carbon (C). However, there is a lack of reference sites characterising C exchange dynamics across annual cycles. Based on the Greenland Ecosystem Monitoring (GEM) programme, here we present 9–11 years of flux and ecosystem data across the period 2008–2018 from two wetland sites in Greenland: Zackenberg (74°N) and Kobbefjord (64°N). The Zackenberg fen was a strong C sink despite its higher latitude and shorter growing seasons compared to the Kobbefjord fen. On average the ecosystem in Zackenberg took up ∼−50 g C m⁻² yr⁻¹ (range of +21 to −90 g C m⁻² yr⁻¹), more than twice that of Kobbefjord (mean ∼−18 g C m⁻² yr⁻¹, and range of +41 to − 41 g C m⁻² yr⁻¹). The larger net carbon sequestration in Zackenberg fen was associated with higher leaf nitrogen (71%), leaf area index (140%), and plant quality (i.e. C:N ratio; 36%). Additional evidence from in-situ measurements includes 3 times higher levels of dissolved organic carbon in soils and 5 times more available plant nutrients, including dissolved organic nitrogen (N) and nitrates, in Zackenberg. Simulations using the soil-plant-atmosphere ecosystem model showed that Zackenberg’s stronger CO₂ sink could be related to measured differences in plant nutrients, and their effects on photosynthesis and respiration. The model explained 69% of the variability of net ecosystem exchange of CO₂, 80% for photosynthesis and 71% for respiration over 11 years at Zackenberg, similar to previous results at Kobbefjord (73%, 73%, and 50%, respectively, over 8 years). We conclude that growing season limitations of plant phenology on net C uptake have been more than counterbalanced by the increased leaf nutrient content at the Zackenberg site.