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Nitrous oxide (N2O) emissions from agriculture are rising due to increased fertilizer use and intensive farming, posing a major challenge for climate mitigation. This study introduces a novel reinforcement learning (RL) framework to optimize farm management strategies that balance crop productivity with environmental impact, particularly N2O emissions. By modeling agricultural decision-making as a partially observable Markov decision process (POMDP), the framework accounts for uncertainties in environmental conditions and observational data. The approach integrates deep Q-learning with recurrent neural networks (RNNs) to train adaptive agents within a simulated farming environment. A Probabilistic Deep Learning (PDL) model was developed to estimate N2O emissions, achieving a high Prediction Interval Coverage Probability (PICP) of 0.937 within a 95% confidence interval on the available dataset. While the PDL model’s generalizability is currently constrained by the limited observational data, the RL framework itself is designed for broad applicability, capable of extending to diverse agricultural practices and environmental conditions. Results demonstrate that RL agents reduce N2O emissions without compromising yields, even under climatic variability. The framework’s flexibility allows for future integration of expanded datasets or alternative emission models, ensuring scalability as more field data becomes available. This work highlights the potential of artificial intelligence to advance climate-smart agriculture by simultaneously addressing productivity and sustainability goals in dynamic real-world settings.