Abstract Vinasse is a residue from bioethanol production that is produced in large quantities in Brazil and Europe and is applied to fields as a source of plant nutrients (fertirrigation). A side effect of this use is greenhouse gas (GHG) emissions during storage and transport in open channels to fields, and from fertirrigated soils. This study assessed GHG emissions in experiments simulating this vinasse management system, and the potential for reducing emissions of methane (CH4) and nitrous oxide (N2O) from vinasse via anaerobic digestion (AD) in biogas plants. During 21 days’ storage of untreated vinasse, 29% of dry matter (DM) and 40% of volatile solids (VS) were lost, which resulted in cumulative CH4 emissions of up to 43.8 kg CO2eq kg−1 C-vinasse. In contrast, there were no CH4 emissions from AD-treated vinasse (digestate) during storage. GHG emission was related to the biochemical characteristics of the untreated and digested vinasse. The accumulation of oxidised nitrogen (N) compounds was up to four-fold higher in soil amended with untreated vinasse than from digestate-amended soil. The N2O emissions from soil amended with untreated vinasse were also higher than from soil amended with digestate, ranging from 0.173 to 0.193 kg CO2eq m−2 in the former and from 0.045 to 0.100 kg CO2eq m−2 in the latter. Extrapolation of the results to a Brazilian case indicated that AD treatment prior to storage/transport and field application could reduce GHG emissions from the vinasse management chain by at least 48%, with further reductions from the use of biogas in power production.