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 with late maturing Dioscorea rotundata -‘Kokoro’ (1-year fallow of Andropgon gayanus-yam rotation, Maize+ 100 kg N14P23K14 + 50 kg Urea –yam rotation) with yam-based cropping systems integrating legumes (Aeschynomene histrix /maize intercropping + 100 kg N14P23K14 + 50 kg Urea –yam rotation and Mucuna pruriens var utilis/maize intercropping + 100 kg N14P23K14 + 50 kg Urea –yam rotation) in a 4-year experiment comprising two year rotations. The objective of the study was to assess the nutrients budget of the sedentary yam-based cropping systems with herbaceous legumes and highlight interactions between factors. 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. Yam based cropping systems with legumes improved significantly the N, P, and K balances in comparison with the traditional systems. ANOVA partial nested model showed that Nutrients budgets of nitrogen, phosphorus and potassium differed significantly depending on the factors Treatment (P<0.05), Farmer (P<0.001), and Replication (P<0.001). The factor Site was not significant for nutrients budgets. Year × Treatment (P<0.001), and Year × Site (P<0.001) interactions were significant.