Increasing soil organic carbon (SOC) is widely recognized as a key pathway for climate change mitigation and enhancing soil ecosystem services, but additional carbon farming practices can lead to additional GHG emissions. We propose a process-based SOC module, AresC model, integrated into an agronomic DSS already in use to monitor SOC while optimizing crop management practices and GHG emissions. AresC model estimates SOC dynamics simulating the effects of management practices, including soil tillage, under Mediterranean climatic conditions. The integrated DSS-SOC model is tested in four case studies including arable crops and orchards under different conditions, with a focus on arid Mediterranean areas. The AresC model showed good agreement with the measured values in all conditions with no significant bias or root mean square errors, and Spearman correlation factors very close to 1. A global sensitivity analysis showed that carbon inputs are the dominant driver of SOC. Finally, compared to the RothC model, AresC showed better performance under drier conditions, and no significant differences were observed between the two models in humid conditions. This study, therefore, demonstrates the potential in agricultural carbon accounting applications of the newly developed AresC model integrated into an agronomic DSS to optimize crop management while properly simulating SOC dynamics.