The modeling of continuous transfers of carbon (C) and nitrogen (N) previously published in the literature has paid little attention to the functional role of micro-organisms. In general, only monoculture systems have been modeled. Furthermore, there have been few experiments under field conditions at farm scale, where clear evidence for the benefits of intercropping is lacking. This work focus on mechanistic modeling approaches based on the ecological functioning of the microbial biomass, to quantify the daily exchange of C and N between plant organs, micro-organisms, rhizobial symbionts, soil compartments and the atmosphere in an arable intercropping system. The MOMOS model was validated on C and N data collected from a common bean (Phaseolus vulgaris L. cv. El Djadida) and maize (Zea mays L. cv. Filou) intercropping system. The experiment was performed at two field sites that were chosen with farmers to represent both high and low soil P availability. The results show that all C and N exchanges were successfully predicted at 5% significance and that they depend on the phenological stage, especially the flowering stage. Increased C allocation from photosynthesis to roots contributed to increasing both grain yield and N grain for intercropped maize. C and N stocks in the common bean nodules were lower in intercropping than in monocultures, and this is associated with the decrease of total atmospheric nitrogen (N2) fixation by intercropped common beans, in particular with a high soil P. However, the rate of N2 fixation was higher in the intercrops than in the monoculture when the soil is P-deficient. Micro-organisms were responsible for most of the C losses from the soil to the atmosphere but intercropping significantly reduced the C losses by improving micro-organism C use efficiency. These results uncover the strong link between N and C stocks, confirming the robustness of the newly formulated MOMOS equations that are validated in this paper. This agroecological modeling experiment demonstrated the functional role of microbial biomass, in both the growth of the intercrops crop and their symbiosis, improving the prediction of the daily C and N flows between plant organs, soil compartments and the atmosphere.