Besides causing acidification, acid sulfate (AS) soils contain large nitrogen (N) stocks and are a potential source of N loading to waters and nitrous oxide (N2O) emissions. We quantified the stocks and flows of N, including crop yields, N leaching, and N2O emissions, in a cultivated AS soil in western Finland. We also investigated whether controlled drainage (CD) and sub-irrigation (CDI) to keep the sulfidic horizons inundated can alleviate N losses. Total N stock at 0–100 cm (19.5 Mg ha−1) was smaller than at 100–200 cm (26.6 Mg ha−1), and the mineral N stock was largest below 170 cm. Annual N leaching (31–91 kg N ha−1) plus N in harvested grain (74–122 kg N ha−1) was 148% (range 118–189%) of N applied in fertilizers (90–125 kg N ha−1) in 2011–2017, suggesting substantial N supply from soil reserves. Annual emissions of N2O measured during 2 years were 8–28 kg N ha−1. The most probable reasons for high N2O emission rates in AS soils are concomitant large mineral N pools with fluctuating redox conditions and low pH in the oxidized subsoil, all favoring formation of N2O in nitrification and denitrification. Although the groundwater level was higher in CD and CDI than in conventional drainage, N load and crop offtake did not differ between the drainage methods, but there were differences in emissions. Nitrogen flows to the atmosphere and drainage water were clearly larger than those in non-AS mineral soils indicating that AS soils are potential hotspots of environmental impacts.