Long term fallow is no longer possible in densely populated tropical areas, but legume cover crops can help maintain soil fertility. Our work aimed to study changes in soil carbon in a sandy loam Ultisol in Benin, which involved a 12-year experiment on three maize cropping systems under manual tillage: traditional no-input cultivation (T), mineral fertilized cultivation (NPK), and association with Mucuna pruriens (M). The origin of soil carbon was also determined through the natural abundance of soil and biomass 13C. In T, NPK and M changes in soil carbon at 0-40 cm were -0.2, +0.2 and +1.3 t C ha(-1) yr(-1), with residue carbon amounting to 3.5, 6.4 and 10.0 t C ha(-1) yr(-1), respectively. After 12 years of experimentation, carbon originating from maize in litter-plus-soil (0-40 cm) represented less than 4% of both total carbon and overall maize residue carbon. In contrast, carbon originating from mucuna in litter-plus-soil represented more than 50% of both total carbon and overall mucuna residue carbon in M, possibly due to accelerated mineralization of native soil carbon (priming effect) and slow mulch decomposition. Carbon originating from weeds in litter-plus-soil represented c. 10% of both total carbon and overall weed residue carbon in T and NPK. Thus mucuna mulch was very effective in promoting carbon sequestration in the soil studied.