Brazil meets about 16% of its energy needs with bioethanol and other sugarcane products and leads the world in biofuel energy production. However, there are concerns over the environmental credentials of the sugarcane given the high emissions of nitrous oxide (N2O) − a potent greenhouse gas − associated with its production. We quantify N2O fluxes from a sugarcane experiment in the Brazilian Cerrado over an entire year, comparing the magnitude of response to different fertilizer treatments: mineral nitrogen (N), a liquid residue from bioethanol distillation known as vinasse (V) and a combination of both (NV), on irrigated and nonirrigated plots. We find that soil N2O fluxes in plots subjected to the NV treatment are, on average, at least three times higher than those in the other treatments, resulting in four times the emissions intensity per yield than when mineral N or vinasse were applied alone. We also find that irrigation has a positive effect on N2O emissions in the first two weeks after treatment addition and on annual sugarcane yield. Emission factors, defined as net N emissions as N2O as a percentage of the total mineral N added, vary from 0.05 to 4.6% according to treatment. Sugarcane production in the Cerrado is a significant source of N2O, due to the synergistic effect of mineral N fertilizer and vinasse. Using vinasse as the main fertilizer, or applying N and vinasse at widely spaced intervals are effective strategies for climate change mitigation, plant nutrition, waste management and cost-efficient production.