Soil carbon (C) sequestration rates vary widely in abandoned agricultural lands, and factors determining this variation, beyond climate, soil type, and productivity, are poorly understood. One such factor is soil disturbance by burrowing mammals. Despite being ubiquitous in all grasslands, the impact of burrowing mammals on soil C dynamics is not well understood. We quantified the major ecosystem processes that are influenced by one such burrowing mammal, plains pocket gophers (Geomys bursarius), in old field ecosystems located in east-central Minnesota, USA. We found that pocket gopher abundance varied among old fields and that newly formed gopher mounds covered up to 6% of the soil surface annually. We first measured short-term C pool and flux changes induced by gopher activities. Soil N mineralization did not differ between the soil in gopher mounds and undisturbed soil. However, for the soil under gopher mounds, N mineralization was 30% lower compared with the undisturbed soil. We developed a process model to simulate the long-term gopher disturbance impact on old field soil C accumulation. This simulation showed that pocket gophers reduced both the rate of soil C accumulation and the total C pool. This reduction is primarily driven by reduced plant C input due to the time it requires for the vegetation to recolonize gopher mounds. Soil organic matter (SOM) decomposition changes had only a minor impact. The process model showed that the depth from which burrowing mammals redistribute soil to the surface is a key factor in determining the overall impact on SOM. In total, our study indicated that soil disturbance by burrowing animals could significantly reduce C storage in old field ecosystems when the mammals are mostly active at the surface soil and can be a significant factor in decreasing overall C sequestration after land abandonment. However, at our study site, gopher abundance decreased with abandonment age, which was likely to have been cause by successional vegetation changes, therefore the gopher disturbance-induced reduction in soil C is transient and decreases with abandonment age.