Aims and Background In cereal-legume intercropping, the association is thought to promote nitrogen transfer through more labile rhizodeposits from the legume to the cereal. The role of the microbial community in this process remains poorly studied. Our hypotheses were: (i) intercropping modifies the composition of rhizosphere bacterial communities (ii) rhizosphere microbial community is involved in nitrogen transfer. Methods In a greenhouse experiment, wheat and pea were grown alone or intercropped and 15N-labelled to measure the N transfer. The active components of the heterotrophic bacterial community were assessed by taxon specific RT-qPCR. The genetic structure, density and activity of the microbial nitrifiers were analyzed respectively by molecular fingerprinting, qPCR of all functional genes (AOA, AOB and nxrA) and potential nitrification rates Results The rhizosphere bacterial community of the intercropped species showed a certain level of specificity, characterized by changes in the relative abundance of three out of seven analyzed phyla (Actinobacteria, Acidobacteria and α-proteobacteria). The amount of 15N transferred between the two crops was small. Nevertheless, a significant increase in specific nitrification rates was noticed in the rhizosphere of intercropped species. Conclusion Intercropping yields a specific microbial environment, which could not be reduced to a simple mixture of pea’s and wheat’s rhizosphere