As the Arctic warms, the ~277 Pg of carbon stored in permafrost peatlands faces an uncertain fate. Arctic and Subarctic peatlands are likely to release more methane (CH4) as permafrost thaw releases formerly-frozen carbon, thaw-induced land subsidence and inundation lead to anaerobic conditions, and higher temperatures allow more rapid decomposition. In addition to these effects, CH4 and carbon dioxide (CO2) emissions may also change due to shifts in plant inputs and consequent changes in organic matter quality, but the exact relationships between organic matter and CH4 production are not well understood. In this study, we examined microbial CH4 and CO2 production and their relationship to organic matter chemistry in Stordalen Mire, a thawing Subarctic peatland in northern Sweden. We also used stable carbon isotopes (δ13C) of CH4 and CO2, and their apparent fractionation factor (αC), to examine the effect of thaw on the proportion of methanogenesis by hydrogenotrophic or acetoclastic pathways. At Stordalen, permafrost thaw causes dry, aerobic permafrost plateaus (palsas) to collapse and become inundated. These wet depressions are then colonized first by Sphagnum mosses and then by sedges as permafrost thaw and plant succession progress. In our study, we examined a chronosequence of sites with varying permafrost status and plant community composition. These sites included dry, intact palsas; recently-thawed collapsed palsa sinkholes; partially-thawed Sphagnum-dominated bogs; mostly-thawed poor fens with a combination of Sphagnum and tall sedges; and fully-thawed rich fens with mature stands of tall sedges and no Sphagnum. The changes in potential CH4 and CO2 production along the thaw progression were examined with anaerobic peat incubations, which were all performed with identical temperature and water saturation. These incubations showed increases in potential decomposition rates and CH4/CO2 production ratios along the thaw progression. Methanogenesis pathways also shifted from predominately hydrogenotrophic to acetoclastic, as revealed by lower αC in fens. These shifts are consistent with increasing organic matter bioavailability along the thaw progression, which was confirmed by analyses of peat and dissolved organic matter (DOM) chemistry. These analyses showed that compared to collapsed palsas and bogs, rich fens had lower peat C/N ratios, higher peat humification rates (as determined by Fourier-transform infrared [FTIR] spectroscopy), and more labile DOM compounds (as determined by Fourier-transform ion cyclotron resonance mass spectrometry [FT-ICR MS]). The validity of these incubations for revealing trends in in situ CH4 and CO2 production was determined by comparison with dissolved CH4 and CO2 in field-collected pore water. The incubation CH4/CO2 ratios were compared to both the raw pore water CH4/CO2 concentration ratios, and to the pore water CH4/CO2 production ratios estimated with an isotope mass balance model. In both cases, CH4/CO2 ratios were higher in the incubations than in the pore water; however, the same increases in CH4/CO2 with thaw were observed in both cases. Incubation and field pore water αC were also compared. Incubation αC values were slightly higher than field αC, but αC decreased with thaw in both the incubations and the field. We thus conclude that incubations can reliably estimate relative CH4/CO2 ratios and αC between different sites, though their ability to estimate absolute CH4/CO2 and αC is limited. The changes in DOM chemistry along the thaw progression were examined more closely with a combination of elemental composition (via FT-ICR MS) and optical properties (via UV/Vis absorption and fluorescence spectroscopies). These techniques revealed that the presence of dense Sphagnum moss, which is abundant in collapsed palsa, bog, and poor fen sites, is the main driver of DOM elemental composition and optical properties at Stordalen. Compared to rich fens, DOM from sites with Sphagnum had greater aromaticity, higher average molecular weights, and greater O/C ratios. These properties suggest a higher abundance of phenolic compounds, which are released by Sphagnum and may inhibit decomposition at these sites. In contrast, rich fen DOM had greater saturation, lower O/C ratios, greater N/C and S/C ratios, and optical properties suggesting a higher proportion of microbially-derived DOM. Overall, our results suggest that the changes in plant community due to permafrost thaw at Stordalen lead to greater organic matter lability and higher CH4 production. In inundated sites, these changes are primarily driven by the disappearance of Sphagnum as partially-thawed sites transition to fully-thawed rich fens. Similar plant successions have been observed in other peatlands with thawing permafrost, highlighting the potential importance of these shifts in driving future northern peatland greenhouse gas balances. Future models of climate feedbacks in permafrost peatlands should thus take into account any changes in plant community composition, especially changes in Sphagnum cover, as permafrost thaws.