Limited knowledge about how nitrogen (N) dynamics are affected by climate change, weather variability, and crop management is a major barrier to improving the productivity and environmental performance of soybean-based cropping systems. To fill this knowledge gap, we created a systems understanding of agroecosystem N dynamics and quantified the impact of controllable (management) and uncontrollable (weather, climate) factors on N fluxes and soybean yields. We performed a simulation experiment across 10 soybean production environments in the United States using the Agricultural Production Systems sIMulator (APSIM) model and future climate projections from five global circulation models. Climate change (2020–2080) increased N mineralization (24%) and N2O emissions (19%) but decreased N fixation (32%), seed N (20%), and yields (19%). Soil and crop management practices altered N fluxes at a similar magnitude as climate change but in many different directions, revealing opportunities to improve soybean systems’ performance. Among many practices explored, we identified two solutions with great potential: improved residue management (short-term) and water management (long-term). Inter-annual weather variability and management practices affected soybean yield less than N fluxes, which creates opportunities to manage N fluxes without compromising yields, especially in regions with adequate to excess soil moisture. This work provides actionable results (tradeoffs, synergies, directions) to inform decision-making for adapting crop management in a changing climate to improve soybean production systems.