AbstractArctic permafrost ecosystems store ~50% of global belowground carbon (C) that is vulnerable to increased microbial degradation with warmer active layer temperatures and thawing of the near surface permafrost. We used anoxic laboratory incubations to estimate anaerobic CO2 production and methanogenesis in active layer (organic and mineral soil horizons) and permafrost samples from center, ridge and trough positions of water‐saturated low‐centered polygon in Barrow Environmental Observatory, Barrow AK, USA. Methane (CH4) and CO2 production rates and concentrations were determined at −2, +4, or +8 °C for 60 day incubation period. Temporal dynamics of CO2 production and methanogenesis at −2 °C showed evidence of fundamentally different mechanisms of substrate limitation and inhibited microbial growth at soil water freezing points compared to warmer temperatures. Nonlinear regression better modeled the initial rates and estimates of Q10 values for CO2 that showed higher sensitivity in the organic‐rich soils of polygon center and trough than the relatively drier ridge soils. Methanogenesis generally exhibited a lag phase in the mineral soils that was significantly longer at −2 °C in all horizons. Such discontinuity in CH4 production between −2 °C and the elevated temperatures (+4 and +8 °C) indicated the insufficient representation of methanogenesis on the basis of Q10 values estimated from both linear and nonlinear models. Production rates for both CH4 and CO2 were substantially higher in organic horizons (20% to 40% wt. C) at all temperatures relative to mineral horizons (<20% wt. C). Permafrost horizon (~12% wt. C) produced ~5‐fold less CO2 than the active layer and negligible CH4. High concentrations of initial exchangeable Fe(II) and increasing accumulation rates signified the role of iron as terminal electron acceptors for anaerobic C degradation in the mineral horizons.