The modeling of carbon (C) and nitrogen (N) fluxes between microorganisms and plants in pure and associated cultures of durum wheat and faba bean demonstrated a close link between the C and N cycles in agroecosystems. The MOMOS (microorganisms and organic matter of soils) model integrates simplified descriptions of photosynthesis (origin of organic C in soil), N microbial exchange (soil origin for N), N fixation (atmospheric origin for N), and plant growth with an organic matter decomposition core that has the soil microbial community at its center. This work provides estimates of the exchange parameters between plant organs and microbes, which were compared to literature data when available. In a connection with photosynthesized C, the root demand for inorganic N can be adjusted by its microbial production. Our approach is a new methodology for improving plant production, by optimizing the interactions with soil microorganisms. Additionally, the coupling of plant growth and microbial processes enabled determining changes of the organic compartments of soil. In the unfertilized limestone soil of this study, sequestration was found to be located in the labile microbial metabolites for one year, then significantly transferred to stable humus during 6-year intercropping. Thus, we propose the MOMOS mathematical tool, not only for guiding ecological intensification, but also related to the management of agroecosystems for climate change mitigation.