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Abstract Large stocks of soil carbon (C) and nitrogen (N) in northern permafrost soils are vulnerable to remobilization under climate change. However, there are large uncertainties in present‐day greenhouse gas (GHG) budgets. We compare bottom‐up (data‐driven upscaling and process‐based models) and top‐down (atmospheric inversion models) budgets of carbon dioxide (CO₂), methane (CH₄) and nitrous oxide (N₂O) as well as lateral fluxes of C and N across the region over 2000–2020. Bottom‐up approaches estimate higher land‐to‐atmosphere fluxes for all GHGs. Both bottom‐up and top‐down approaches show a sink of CO₂in natural ecosystems (bottom‐up: −29 (−709, 455), top‐down: −587 (−862, −312) Tg CO₂‐C yr⁻¹) and sources of CH₄(bottom‐up: 38 (22, 53), top‐down: 15 (11, 18) Tg CH₄‐C yr⁻¹) and N₂O (bottom‐up: 0.7 (0.1, 1.3), top‐down: 0.09 (−0.19, 0.37) Tg N₂O‐N yr⁻¹). The combined global warming potential of all three gases (GWP‐100) cannot be distinguished from neutral. Over shorter timescales (GWP‐20), the region is a net GHG source because CH₄dominates the total forcing. The net CO₂sink in Boreal forests and wetlands is largely offset by fires and inland water CO₂emissions as well as CH₄emissions from wetlands and inland waters, with a smaller contribution from N₂O emissions. Priorities for future research include the representation of inland waters in process‐based models and the compilation of process‐model ensembles for CH₄and N₂O. Discrepancies between bottom‐up and top‐down methods call for analyses of how prior flux ensembles impact inversion budgets, more and well‐distributed in situ GHG measurements and improved resolution in upscaling techniques.