Recent studies have shown that electrolysis can be an efficient process for nitrogen removal from urine. These studies have been conducted with urea solutions or fresh urine, but urine collected in NoMix toilets and urinals has a substantially different composition, because bacteria hydrolyse urea quickly to ammonia and carbonate. In this study, we compared electrochemical removal of nitrogen from synthetic solutions of fresh and stored urine using IrO2 anodes. We could show that in fresh urine both ammonia and urea are efficiently eliminated, mainly through chlorine-mediated oxidation. However, in stored urine the presence of carbonate, arising from urea hydrolysis, leads to an inhibition of ammonia oxidation. We suggest two parallel mechanisms to explain this effect: the competition between chloride and carbonate oxidation at the anode and the competition between chlorate formation, enhanced by the buffering effect of carbonate, and ammonia oxidation for the consumption of active chlorine in the bulk. However, further experiments are needed to support the latter mechanism. In conclusion, this study highlights the negative consequences of the presence of carbonate in urine solutions, but also in other wastewaters, when subjected to an electrolytic treatment on IrO2 in alkaline media.