Abstract Aims High nitrogen (N) fertiliser inputs in intensive sugarcane systems drive productivity but also significant emissions of nitrous oxide (N₂O), a potent greenhouse gas. Fertiliser and soil N availability for both plant N uptake and N₂O emissions across different N rates remain unknown, hindering efficient N management. This study investigated the contribution of fertiliser and soil N and their interaction to plant N uptake and N₂O emissions in two intensively managed tropical sugarcane systems. Methods High temporal resolution N₂O measurements were combined with ¹⁵N recoveries across four N fertiliser rates, (100, 150, 200 and 250 kg N ha^{− 1}) in soil, plant and N₂O emissions. Results Cumulative N₂O emissions ranged from 0.3 to 4.1 kg N ha^{− 1}, corresponding to emission factors ranging from 0.7 to 2.4%. Native soil N accounted for > 60% of cumulative N₂O emissions and total plant N uptake. Fertiliser N addition increased N₂O emissions from native soil N compared to the unfertilised control, highlighting the interaction between fertiliser and soil N, which determined the overall magnitude but also the response of total N₂O emissions to N rates dependent on the site conditions. Overall fertiliser ¹⁵N loss responded exponentially to N rates with 50% of applied N fertiliser permanently lost even at the recommended N rate. Conclusions The interaction between fertiliser and soil N and its contribution to N uptake and N₂O emissions demonstrate the importance of integrating soil fertility management with N fertiliser rate recommendations for sugarcane systems to maintain crop productivity and reduce environmental impacts.