Description: Background and aims Legumes integrated in crop rotations are intended to improve crop nitrogen (N) supply and yield. In conservation agriculture (CA) systems under low input conditions on highly weathered tropical soils, experimental evidence for these benefits is lacking. To understand the mechanisms and evaluate the impact of the legume N on the subsequent crop, an in-depth study on N dynamics in the soil-plant system was conducted. Methods In Madagascar, a CA based crop rotation with the perennial forage legume Stylosanthes guianensis (stylo) and upland rice (rice/stylo – stylo - rice/stylo) was established under three fertilization regimes. In addition, rice was grown in a non-CA bare fallow rotation without fertilizer. Over the three years N 2 fixed in stylo shoots, the incorporation of stylo shoot (mulch) N into soil N pools and mulch N uptake by rice was quantified using 15 N techniques and mulch and stylo root residue decomposition was investigated in a litterbag study. Results N 2 fixed in stylo shoots ranged from 96 to 122 kg N ha −1 . Between 50 to 70% of stylo mulch and root residues decomposed during the third cropping season. Without fertilizer, grain yield of rice after the fallow with stylo was about 70% greater than after bare fallow, corresponding to 11 kg N ha −1 greater N uptake. Recoveries of stylo mulch N after rice harvest were on average 64% in soil, with about 3% in each of the microbial and mineral N pools, with 39% on the soil surface, and 6% in the rice crop. The N input via stylo seed, leaf litter and belowground N totalled about three times the amount of N contained in stylo mulch, which usually is considered as major rice N source. Conclusions Legumes, like stylo, can improve crop N supply and yield in low input CA cropping systems on highly weathered tropical soils. To explain the impact and mechanisms involved requires a consideration of all legume-N components beyond the mulch N present at the onset of the rice-cropping season.