The long-term net sink of carbon (C), nitrogen (N) and greenhouse gases (GHGs) in the northern permafrost region is projected to weaken or shift under climate change. But large uncertainties remain, even on present-day GHG budgets. We compare bottom-up (data-driven upscaling, process-based models) and top-down budgets (atmospheric inversion models) of the main GHGs (CO2, CH4, and N2O) and lateral fluxes of C and N across the region over 2000-2020. Bottom-up approaches estimate higher land to atmosphere fluxes for all GHGs compared to top-down atmospheric inversions. Both bottom-up and top-down approaches respectively show a net sink of CO2 in natural ecosystems (-31 (-667, 559) and -587 (-862, -312), respectively) but sources of CH4 (38 (23, 53) and 15 (11, 18) Tg CH4-C yr-1) and N2O (0.6 (0.03, 1.2) and 0.09 (-0.19, 0.37) Tg N2O-N yr-1) in natural ecosystems. Assuming equal weight to bottom-up and top-down budgets and including anthropogenic emissions, the combined GHG budget is a source of 147 (-492, 759) Tg CO2-Ceq yr-1 (GWP100). A net CO2 sink in boreal forests and wetlands is offset by CO2 emissions from inland waters and CH4 emissions from wetlands and inland waters, with a smaller additional warming from N2O emissions. Priorities for future research include representation of inland waters in process-based models and compilation of process-model ensembles for CH4 and N2O. Discrepancies between bottom-up and top-down methods call for analyses of how prior flux ensembles impact inversion budgets, more in-situ flux observations and improved resolution in upscaling.

East Asia (China, Japan, Koreas and Mongolia) has been the world’s economic engine over at least the past two decades, exhibiting a rapid increase in fossil fuel emissions of greenhouse gases (GHGs) and has expressed the recent ambition to achieve climate neutrality by mid-century. However, the GHG balance of its terrestrial ecosystems remains poorly constrained. Here, we present a synthesis of the three most important long-lived greenhouse gases (CO2, CH4 and N2O) budgets over East Asia during the decades of 2000s and 2010s, following a dual constraint bottom-up and top-down approach. We estimate that terrestrial ecosystems in East Asia is close to neutrality of GHGs, with a magnitude of between 196.9 ± 527.0 Tg CO2eq yr-1 (the top-down approach) and -20.8 ± 205.5 Tg CO2eq yr-1 (the bottom-up approach) during 2000-2019. This net GHG emission includes a large land CO2 sink (-1251.3 ± 456.9 Tg CO2 yr-1 based on the top-down approach and -1356.1 ± 155.6 Tg CO2 yr-1 based on the bottom-up approach), which is being fully offset by biogenic CH4 and N2O emissions, predominantly coming from the agricultural sector. Emerging data sources and modelling capacities have helped achieve agreement between the top-down and bottom-up approaches to within 20% for all three GHGs, but sizeable uncertainties remain in several flux terms. For example, the reported CO2 flux from land use and land cover change varies from a net source of more than 300 Tg CO2 yr-1 to a net sink of ~-700 Tg CO2 yr-1.