Agroecological practices, including growing cover crops, are promising practices to adapt to climate change and mitigate greenhouse gas (GHG) emissions. However, their long-term effects on soil nitrogen (N) dynamics and mineral N fertilization in cropping systems requires further investigation. Using a simulation approach, we investigated their long-term effects on maize production, N fertilization requirements, N dynamics, GHG emissions and soil carbon storage. The integrated modeling framework we developed, STICS-TK-R, which includes decision rule models, the STICS crop model, the MERCI decision tool for cover crop residues and an N-balance model for mineral fertilization, enables comprehensive analysis and comparison of agroecological systems. In the context of projected climate change (2016-2050), we simulated six agroecological scenarios that combined two mineral N fertilization practices (i.e., fixed or balanced) and three fallow-period management practices (i.e., bare soil, long legume cover crops or cruciferous cover crops) for five diverse soil and climate conditions in southwestern France.