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A field study was conducted in the sub-humid tropical region of India to examine the effect of different nitrogen (N) management strategies on nitrate leaching, nitrous oxide (N2O) emission and N use efficiency in aerobic rice. Treatments were: control (no N), 120 kg N ha−1 applied as prilled urea (PU) in conventional method, 120 kg N ha−1 applied as neem coated urea (NCU) in conventional method, N applied as PU on the basis of leaf colour chart (LCC) reading, N applied as NCU on the basis of LCC reading, and 120 kg N ha−1 applied as PU and farm yard manure (FYM) in 1:1 ratio. Results showed that 3.4–16.1 kg NO3-N ha−1 was leached below 45 cm depth and 0.61–1.12 kg N2O-N ha−1 was emitted from aerobic rice during the growing season. NCU when applied conventionally reduced nitrate-nitrogen (NO3-N) leaching and N2O emission by 18.6% and 21.4%, respectively However when applied on the basis of LCC reading NCU reduced NO3-N leaching by 39.8% as compared to PU applied in conventional method. NCU when applied on the basis of LCC reading synchronized N supply with demand and reduced N loss, which resulted in higher yield and N use efficiency.ICA