Integration of the priming effect (PE) in ecosystem models is crucial to better predict the consequences of global change on ecosystem carbon (C) dynamics and its feedbacks on climate. Over the last decade, many attempts have been made to model PE in soil and its underlying mechanisms. However, PE has not yet been incorporated into any ecosystem models. Here we build plant-soil models to explore how PE and microbial diversity influence soil-plant interactions and ecosystem C and nitrogen (N) dynamics in response to global change (elevated CO2 and increased atmospheric N deposition). Our results show that plant persistence, soil organic matter (SOM) accumulation and low N leaching in undisturbed ecosystems relies on a fine adjustment of microbial N mineralization to plant N uptake. This adjustment can be modeled in the SYMPHONY model by considering the destruction of SOM through PE and the interactions between two distinct microbial functional groups: SOM-decomposers and SOM-builders. After estimation of parameters, SYMPHONYprovided realistic predictions on forage production, soil C storage and N leaching for a permanent grassland. Consistent with recent observations, SYMPHONY predicted a CO2-induced modification of soil microbial communities leading to an intensification of SOM mineralization and a decrease in the soil C stock. SYMPHONY also indicated that atmospheric N deposition may stimulate SOM accumulation via changes in the structure and metabolic activities of microbial communities. Collectively, these results suggest that PE and the functional role of microbial diversity may be incorporated in current ecosystem models with a few additional parameters, improving accuracy of predictions.