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Aims Previous cover crop studies mainly focused on the links between plant uptake and soil fertility, and there is a clear knowledge gap regarding the role of microbes in these processes. Our aim was then to better understand the effects of plant mixtures (versus monoculture) and the specific effects of each plant species on nitrogen (N) and phosphorus (P) partitioning between plant, soil, and more particularly microbial pools. Methods Monocultures and mixtures composed of black oat, field pea and Indian mustard were grown during two months in a greenhouse. The concentrations of carbon (C), N and P were measured in both plant and microbial biomass at final harvest, together with soil available N and P. Results Overall, our findings highlight stronger selection effect (i.e., presence of key species) rather than complementarity effects (i.e., species mixture) to affect the measured parameters. The presence of pea increased the biomass production of oat and mustard, as well as the nutrient concentration of oat, whereas pea P concentration decreased in presence of oat and mustard N and P concentrations were negatively impacted respectively by the presence of oat and pea. We also observed a strong competition between plants and microbes for both soil N and P. Conclusions The oat-pea and the oat-pea-mustard mixtures represented the best compromise between biomass production, nutrient storage and biomass C:N ratio, thus insuring a good organic matter decomposition and nutrient provision for the following main crop.