Stordalen Mire is a peatland in the discontinuous permafrost zone in arctic Sweden that exhibits a habitat gradient from permafrost palsa, to Sphagnum bog underlain by permafrost, to Eriophorum-dominated fully thawed fen. We used three independent approaches to evaluate the annual, multi-decadal, and millennial apparent carbon accumulation rates (aCAR) across this gradient: seven years of direct semi-continuous measurement of CO₂ and CH₄ exchange, and 21 core profiles for ²¹⁰Pb and ¹⁴C peat dating. Year-round chamber measurements indicated net carbon balance of −13 ± 8, −49 ± 15, and −91 ± 43 g C m⁻² y⁻¹ for the years 2012–2018 in palsa, bog, and fen, respectively. Methane emission offset 2%, 7%, and 17% of the CO₂ uptake rate across this gradient. Recent aCAR indicates higher C accumulation rates in surface peats in the palsa and bog compared to current CO₂ fluxes, but these assessments are more similar in the fen. aCAR increased from low millennial-scale levels (17–29 g C m⁻² y⁻¹) to moderate aCAR of the past century (72–81 g C m⁻² y⁻¹) to higher recent aCAR of 90–147 g C m⁻² y⁻¹. Recent permafrost collapse, greater inundation and vegetation response has made the landscape a stronger CO₂ sink, but this CO₂ sink is increasingly offset by rising CH₄ emissions, dominated by modern carbon as determined by ¹⁴C. The higher CH₄ emissions result in higher net CO_2-equivalent emissions, indicating that radiative forcing of this mire and similar permafrost ecosystems will exert a warming influence on future climate.