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Drylands are expanding globally under climate change, intensifying pressures on soil organic carbon (SOC) and nutrient cycling in agricultural landscapes. In Brazil, semi-arid agroecosystems already experience recurrent droughts, high temperatures, and structural soil constraints, making carbon–nutrient dynamics highly vulnerable to warming and drying trends. Process-based ecosystem models are essential tools for evaluating the long-term sustainability of land-use strategies in these fragile environments. This study applied the DayCent model to quantify SOC and nitrogen (N) trajectories from 2024 to 2100 under the current climate and two IPCC scenarios (SSP2-4.5 and SSP5-8.5) across three representative dryland regions: Betânia do Piauí, Petrolina, and Sobral, each encompassing contrasting soil textures, land-use histories, and intensification agricultural gradients. Model calibration used field-measured SOC and N stocks (0–30 cm), soil properties, and detailed management records from native vegetation, conventional systems, grazed pastures, crop–livestock integration (CLI), and crop–livestock–forestry integration (CLFI). DayCent showed strong performance (SOC: R² = 0.97, RMSE = 2.09 Mg C ha⁻¹; N: R² = 0.73, RMSE = 0.55 Mg N ha⁻¹), indicating robust capacity to reproduce observed carbon–nitrogen stocks in these semi-arid systems. Simulations revealed that conversion of native vegetation, especially when associated with fire or low-input management, reduced SOC stocks by 5–20%. In contrast, agricultural intensification enhanced SOC in all regions, though responses varied by site and soil texture. In Betânia, integrated crop-livestock systems with annual fertilization combined with no-till farming stored approximately 37% more SOC stocks (75 Mg C ha⁻¹) compared to conventional tillage with fertilization every 5 years. In Petrolina, reduced grazing pressure and N fertilization increased SOC stocks relative to current grazing systems, while in Sobral, no-tillage consistently reduced SOC losses compared to conventional tillage, particularly in intercropping systems. Across all sites, climate change simulations showed pervasive SOC declines under SSP2-4.5 and SSP5-8.5, with the most pronounced losses under the high-emission scenario. Reductions were strongest in sandy soils and in systems with frequent soil disturbance. Although management intensification (fertilization, reduced grazing, and no-tillage) consistently mitigated SOC losses, no strategy fully compensated for the negative impacts of increased aridity and reduced precipitation. Integrated agricultural systems were the most resilient, partially buffering climate-induced SOC stock declines through greater biomass inputs. Overall, the results demonstrate that sustainable intensification can enhance SOC under present conditions, future climate change will reduce SOC stocks across all systems, and integrated and conservation-based strategies remain essential for slowing carbon depletion in Brazilian drylands. These findings highlight the need for climate-smart soil management policies focused on minimizing soil disturbance, enhancing nutrient availability, and increasing organic inputs to maintain carbon-nutrient resilience under intensifying aridity.