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The beneficial effect of intercropping system under low phosphorus (P) conditions has already been reported in previous works. The aim of this study was to test the hypothesis that intercropping (common bean - maize) in P-deficient soil can enhance the carbon (C) and nitrogen (N) stocks from the microbial biomass (MB). The field experiment was conducted in Setif province in a northern Algerian agroecosystem with a Mediterranean climate. The nodule N storage in intercropped common bean was 60% higher than for sole crops and was highest in a P-deficient soil in the second year. The carbon stock from the microbial biomass of the soil (MBC) was higher with intercropping than for sole crops and fallow and was even higher in P-deficient (23%) soils as compared to P sufficient (17%) conditions. There was a strong correlation between C stock from nodule (NC) and MBC stock for intercropping in either P-deficient (r 2 = 0.80***; p < 0.001) or P-sufficient soils (r 2 = 0.69**; p < 0.01). P-deficient conditions gave the highest total soil respiration (1.68 g C-CO 2 m −2 days −1 ) and the lowest MB C:N ratio (10.3 and 12.2 for common bean and maize, respectively) in intercrops system. This study showed that, in a P-deficient soil, intercropping is a good solution for increasing the rhizosphere MB through C and N partitioning between root nodules and rhizosphere microbial community, which is responsible for improving soil fertility and recycle mineral elements. [ABSTRACT FROM AUTHOR]