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Boreal-Arctic regions are key stores of organic carbon (C) and play a major role in the greenhouse gas balance of high-latitude ecosystems. The carbon-climate (C-climate) feedback potential of northern high-latitude ecosystems remains poorly understood due to uncertainty in temperature and precipitation controls on carbon dioxide (CO2) uptake and the decomposition of soil C into CO2 and methane (CH4) fluxes. While CH4 fluxes account for a smaller component of the C balance, the climatic impact of CH4 outweighs CO2 (28–34 times larger global warming potential on a 100-year scale), highlighting the need to jointly resolve the climatic sensitivities of both CO2 and CH4. Here, we jointly constrain a terrestrial biosphere model with in situ CO2 and CH4 flux observations at seven eddy covariance sites using a data-model integration approach to resolve the integrated environmental controls on land-atmosphere CO2 and CH4 exchanges in Alaska. Based on the combined CO2 and CH4 flux responses to climate variables, we find that 1970-present climate trends will induce positive C-climate feedback at all tundra sites, and negative C-climate feedback at the boreal and shrub fen sites. The positive C-climate feedback at the tundra sites is predominantly driven by increased CH4 emissions while the negative C-climate feedback at the boreal site is predominantly driven by increased CO2 uptake (80% from decreased heterotrophic respiration, and 20% from increased photosynthesis). Our study demonstrates the need for joint observational constraints on CO2 and CH4 biogeochemical processes—and their associated climatic sensitivities—for resolving the sign and magnitude of high-latitude ecosystem C-climate feedback in the coming decades.