CONTEXT 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. OBJECTIVE Using a simulation approach, we investigated their long-term effects on maize production, N fertilization requirements, N dynamics, GHG emissions and soil carbon storage. METHODS 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, legume cover crops or cruciferous cover crops with long growing period duration, from 5 to 7 months) for five diverse soil and climate conditions in southwestern France. RESULTS AND CONCLUSION The framework predicted significant advancement of sowing, fertilization and harvest dates of the main crop, without decreasing its yields. Nitrogen fertilization requirements varied among scenarios and sites. In particular, a faba bean cover crop decreased N fertilization requirements greatly over time. Analysis of N balance components highlighted the influence of increased soil organic matter and cover crop residues on N mineralization and the importance of adjusting fertilization practices to maintain certain services or offset certain environmental impacts over time (e.g., nitrate leaching, nitrous oxide emissions, GHG emissions). STICS-TK-R was thus able to determine N fertilization rates in different contexts over the long-term. SIGNIFICANCE We highlight the importance of adapting agricultural strategies and emphasize the need to adjust (dynamically and locally) N fertilization in agroecological systems in the context of climate change to optimize agronomic and environmental performances, especially the GHG balance.