Climate change will directly affect carbon and nitrogen mineralization through changes in temperature and soil moisture, but it may also indirectly affect mineralization rates through changes in soil quality. We used an experimental mesocosm system to examine the effects of 6-year manipulations of infrared loading (warming) and water-table level on the potential anaerobic nitrogen and carbon (as carbon dioxide (CO2) and methane (CH4) production) mineralization potentials of bog and fen peat over 11 weeks under uniform anaerobic conditions. To investigate the response of the dominant methanogenic pathways, we also analyzed the stable isotope composition of CH4 produced in the samples. Bog peat from the highest water-table treatment produced more CO2 than bog peat from drier mesocosms. Fen peat from the highest water-table treatment produced the most CH4. Cumulative nitrogen mineralization was lowest in bog peat from the warmest treatment and lowest in the fen peat from the highest water-table treatment. As all samples were incubated under constant conditions, observed differences in mineralization patterns reflect changes in soil quality in response to climate treatments. The largest treatment effects on carbon mineralization as CO2 occurred early in the incubations and were ameliorated over time, suggesting that the climate treatments changed the size and/or quality of a small labile carbon pool. CH4 from the fen peat appeared to be predominately from the acetoclastic pathway, while in the bog peat a strong CH4 oxidation signal was present despite the anaerobic conditions of our incubations. There was no evidence that changes in soil quality have lead to differences in the dominant methanogenic pathways in these systems. Overall, our results suggest that even relatively short-term changes in climate can alter the quality of peat in bogs and fens, which could alter the response of peatland carbon and nitrogen mineralization to future climate change.