Changes in organic carbon after deforestation in Sahelian soils in Senegal were simulated both retrospectively and prospectively with the RothC model. Retrospective simulation modeling allowed us to recreate organic carbon dynamics during the exploitation period of a cropping system from 1991 to 2009. Beginning with an initial carbon stock equal to that measured in the undisturbed forest (14.8t C ha−1), predicted carbon stocks after 18 years of different crop rotations were of the same order as the mean stock measured in the cropped zone in 2009 (8.1 t C ha−1). The sustainability of the cropping systems that may be established in the future was evaluated with prospective simulation from 2009 to 2080, taking climate change scenarios into account. Rotations of continuous crops, even with fallow periods, led to loss carbon stock of about 5 and 6 t C ha−1, which may involve decrease in land productivity in the long term. Agroforestry systems generated relatively large gains in soil organic carbon, which could render local cropping systems sustainable. The effect of climate change on changes in soil organic carbon appeared of secondary importance compared to inputs of carbon from spontaneous or sown vegetation associated with crop rotations.