The combination of nitritation and autotrophic denitrification (anammox) in a single sequencing batch reactor (SBR) is an energy efficient process for nitrogen removal from high-strength ammonia wastewaters. So far, the process has been successfully applied to digester supernatant. However, the process could also be suitable to treat source-separated urine, which has very high ammonium and organic substrate concentrations (up to 8,200 gN/m3 and 10,000 gCOD/m3). In this study, reactor performance was tested for digester supernatant and diluted source-separated urine. Ammonium concentrations in both solutions were similar (between 611 and 642 gN/m3), thus reactor performance could be directly compared. Differences were mainly due to higher activity of heterotrophic bacteria in urine. Nitrogen removal was slightly higher for source-separated urine, because heterotrophic bacteria denitrified the nitrate that was produced by anammox bacteria. In spite of higher heterotrophic growth with source-separated urine, calculated sludge concentrations at steady state were higher with digester supernatant due to accumulation of inert particulate organic matter from the influent. Although the sludge concentrations are less problematic for source-separated urine, process instabilities are more likely, because lower pH values are reached and heterotrophic denitrification can cause sudden increases of nitrite concentrations and/or nitric oxide. Both compounds inhibit aerobic ammonium oxidizing bacteria, heterotrophic bacteria and, most importantly, anammox bacteria. Nitrite and nitric oxide production by heterotrophic denitrification must be better understood to optimize nitritation/anammox for source-separated urine.