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Abstract Tundra and boreal ecosystems encompass the northern circumpolar permafrost region and are experiencing rapid environmental change with important implications for the global carbon (C) budget. We analysed multi-decadal time series containing 302 annual estimates of carbon dioxide (CO₂) flux across 70 permafrost and non-permafrost ecosystems, and 672 estimates of summer CO₂flux across 181 ecosystems. We find an increase in the annual CO₂sink across non-permafrost ecosystems but not permafrost ecosystems, despite similar increases in summer uptake. Thus, recent non-growing-season CO₂losses have substantially impacted the CO₂balance of permafrost ecosystems. Furthermore, analysis of interannual variability reveals warmer summers amplify the C cycle (increase productivity and respiration) at putatively nitrogen-limited sites and at sites less reliant on summer precipitation for water use. Our findings suggest that water and nutrient availability will be important predictors of the C-cycle response of these ecosystems to future warming.