In West Africa, yam cultivation is now facing increasing scarcity of fertile soils. With the aim of designing more sustainable yam cropping systems in Central Benin, we compared smallholder farmers’ traditional yam-based cropping systems (1-year fallow of Andropogonon gayanus -yam rotation; maize-yam rotation) with yam-based systems with legumes (intercropped Aeschynomene histrix with maize-yam rotation; intercropped Mucuna pruriens with maize-yam rotation) in a 4-year experiment comprising two year rotations. The objective of the study was to assess the organic balance of the sedentary yam-based cropping systems with herbaceous legumes and highlight relationship between soil organic matter, biomass dry matter and yam yields. The experiment was conducted with 32 farmers, eight in each site. For each of them, a randomized complete block design with four treatments and four replicates was carried out using a partial nested model with five factors: Year, Replicate, Farmer, Site, and Treatment. Predicted soil organic matter (SOM) was estimated for the time horizon 40 years, i.e. the life cycle of a farm household in the study area. At the beginning of the experiment (2002), the average amount of humus was 37.88 t ha-1. If this rotational dynamic is sustained over time, the amount of soil humus will increase significantly in herbaceous legume systems (44.72 to 92.52 t ha-1) compared to local systems (32.02 to 69.77 t ha-1). This would result in a total net water balance ranging from 6.15 to 44.78 t ha-1 in improved systems at -5.27 to 36.85 t ha-1 in local systems. The relationship between SOM at (0-10 and 10-20 cm depths) and the total crop biomass incorporated into the soil were significant in improved systems (P<0.01) in comparison with the local. The relationship between yam yields and SOM was significantly higher in improved systems at 0-10 cm depth compared with the local (P<0.01). No relationship between yam yields and SOM was observed at 10-20 cm depth.