Carbon (C) and nitrogen (N) sequestration in plants and soil micro-organisms is considered as a major phenomenon against global warming. The modeling of this phenomenon aims at highlighting the role that the legumes-cereals mixed crop can play in the reduction of greenhouse gases. It is based on field experiments in maize (Zea mays L.)-common bean (Phaseolus vulgaris L.) intercropped system of the cereal agroecosystem in Setif region of Algeria. For this purpose, the MOMOS model was selected and validated in a calcareous soil and low phosphorus (P) conditions. It revealed some mechanisms that control the C and N sequestration in the compartments of the complex soil-plant-atmosphere-microorganism system. CN modeling results show that the daily growth of intercropped maize with common beans is positively correlated with the microbial CN transformation during the cropping cycle, under limited P and N conditions. Thus, this approach revealed the functional role of rhizobial symbiosis in maintaining the balance between the different C and N exchanges from soil to atmosphere and from atmosphere to soil. © 2019, Eesti Pollumajandusulikool. All rights reserved.