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Rapid Arctic warming is causing permafrost to thaw and exposing large quantities of soil organic carbon (C) to potential decomposition. In dry upland tundra systems, subsidence from thawing permafrost can increase surface soil moisture resulting in higher methane (CH4) emissions from newly waterlogged soils. The proportion of C released as carbon dioxide (CO2) and CH4 remains uncertain as previously dry landscapes transition to a thawed state, resulting in both wetter and drier microsites. To address how thaw and moisture interact to affect total C emissions, we measured CH4 and CO2 emissions from paired chambers across thaw and moisture gradients created by nine years of experimental soil warming in interior Alaska. Cumulative growing season (May–September) CH4 emissions were elevated at both wetter (216.1–1,099.4 mg CH4-C m−2) and drier (129.7–392.3 mg CH4-C m−2) deeply thawed microsites relative to shallow thaw (55.6–215.7 mg CH4-C m−2) and increased with higher deep soil temperatures and permafrost thaw depth. Interannual variability in CH4 emissions was driven by wet conditions in graminoid-dominated plots that generated >70% of emissions in a wet year. Shoulder season emissions were equivalent to growing season CH4 emissions rates in the deeply thawed, warmed soils, highlighting the importance of non-growing season CH4 emissions. Net C sink potential was reduced in deeply thawed wet plots by 4%–42%, and by 3.5%–8% in deeply thawed drier plots due to anaerobic respiration, suggesting that some dry upland tundra landscapes may transition into stronger CH4 sources in a warming Arctic.