The release of CH4 and CO2 from thawing permafrost soils will substantially impact the global carbon budget. During anaerobic conditions, these emissions are caused by a complex web of microbes. Depending on their interactions, differing ratios of CH4 to CO2 are produced. In order to predict these emissions, mechanistic modeling of microbial processes is essential but is largely omitted in current climate models. We present a new, process-based model for CH4 and CO2 production in anaerobic permafrost soils after thaw, incorporating key microbial functional types. Each microbial functional type is represented by a specific chemical pathway, allowing the calculation of substance utilization and production stoichiometrically for each time step. To the best of our knowledge, this is the first model incorporating a microbial type utilizing alternative electron acceptors, specifically Fe3+. These microbes out-compete acetoclastic methanogens for acetate as long as Fe3+ is sufficiently abundant, thereby suppressing CH4 production via this pathway. In addition, fermentation can be inhibited by the accumulation of its end product acetate, as has been observed in experiments. We optimize the model parameters against data from an anaerobic permafrost soil incubation experiment over seven years.