and microbiological properties, including enzymatic activity, at different depths and locations perpendicular to the tree line. Results The root biomass and properties were heterogeneous in the young alley-cropping system due to the presence of different plant communities and the heterogeneity of the soil mineral N content according to the location perpendicular to the tree line. The soil microbiological properties and organic C stocks did not vary horizontally at this stage of agroforestry but should be monitored through multiple-time samples to confirm a differentiation in subsequent years suggested by the tight link between root stoichiometry and microbial extracellular enzymatic activities that we found. Conclusions Altogether, our results suggested that increasing the root biomass in topsoil in agroforestry systems positively contributes to increasing soil organic C stocks, but in deeper soil layers, an increase in litter inputs with a high C:N ratio might accentuate microbial N limitations and limit soil C storage.