Peatland soils currently store 455 x 1015 g carbon, approximately 75-times the amount of carbon released annually from fossil fuel burning. In response to future global change, this stored carbon could be released to the atmosphere as carbon dioxide (CO2) and/or methane (CH4) as a result of enhanced microbial decomposition, augmenting anthropogenic emissions of these important greenhouse gases. Thus, understanding the controls of microbial carbon cycling in peatlands has important implications in the context of global climate change. This dissertation focuses on the controls of anaerobic carbon mineralization and aerobic CH4 oxidation in peatland ecosystems. I used an experimental mesocosm system to examine the effects of 6-year manipulations of infrared loading (warming) and water-table level on potential carbon mineralization in bog and fen peat. Peat was incubated under uniform anaerobic conditions in the laboratory, and observed differences in CO2 and CH4 production were attributed to indirect effects of climate through changes in soil quality; however, these changes did not lead to shifts in the dominant pathway of CH4 production. I also used a combination of short-term nutrient amendments and long-term ecosystem fertilizations to demonstrate that nitrogen and phosphorus are important controls of microbial carbon cycling in peatlands; however, the role of these nutrients is strongly mediated by peatland type. For example, in peatlands from northern Michigan, anaerobic carbon mineralization in bog peat was consistently inhibited by increased phosphorus availability, but similar phosphorus additions had few effects in peat from an intermediate fen and stimulated CH4 production in rich fen peat. Finally, I constructed budgets of anaerobic carbon mineralization in a bog, an intermediate fen, and a rich fen from northern Michigan. CH4 production was responsible for between 3 and 70% of anaerobic carbon mineralization and sulfate reduction explained between 2 and 31%. A large proportion of anaerobic carbon mineralization (from 27 to 85%) was unexplained and is likely due to fermentation processes or the use of humic acids as electron acceptors. This dissertation demonstrates that understanding the pathways of microbial carbon cycling is essential to predict the response of peatland ecosystems to global change.