Nitrogen (N) fertilizer use has simultaneously increased global food production and N losses, resulting in degradation of water quality and climate pollution. A better understanding of N application rates and crop and environmental response is needed to optimize management of agroecosystems. Here we show an orchard agroecosystem with high N use efficiency promoted substantial gains in carbon (C) storage, thereby lowering net global warming potential (GWP). We conducted a 5-year whole-system analysis comparing reduced (224 kg N ha^-1 yr^-1) and intensive (309 kg N ha^-1 yr^-1) fertilizer N rates in a California almond orchard. The intensive rate increased net primary productivity (Mg C ha^-1) and significantly increased N productivity (kg N ha^-1) and net N mineralization (mg N kg^-1 soil d^-1). Use of ¹⁵N tracers demonstrated short and long-term mechanisms of soil N retention. These low organic matter soils (0.3-0.5%) rapidly immobilized fertilizer nitrate within 36 h of N application and ¹⁵N in tree biomass recycled back into soil organic matter over five years. Both fertilizer rates resulted in high crop and total N recovery efficiencies of 90% and 98% for the reduced rate, and 72% and 80% for the intensive rate. However, there was no difference in the proportion of N losses to N inputs due to a significant gain in soil total N (TN) in the intensive rate. Higher soil TN significantly increased net N mineralization and a larger gain in soil organic carbon (SOC) from the intensive rate offset nitrous oxide (N₂O) emissions, leading to significantly lower net GWP of -1.64 Mg CO₂-eq ha^-1 yr^-1 compared to -1.22 Mg CO₂-eq ha^-1 yr^-1 for the reduced rate. Our study demonstrates increased N cycling and climate mitigation from intensive fertilizer N use in this orchard agroecosystem, implying a fundamentally different result than seen in conventional annual cropping systems.

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