Urine contains nutrients which can be applied usefully as a fertiliser in agriculture, but the relatively high pH can lead to ammonia evaporation. Electrodialysis with bipolar membranes was combined with an additional mass transfer unit in order to render a product containing ammonium and phosphate at a low pH. In one case, the additional mass transfer unit consisted of bubble columns placed in acid and basic concentrate streams, connected with a circulating gas phase. In the other case, the unit consisted of a gas-filled (hydrophobic) membrane placed in between the circulating acid and basic concentrate streams. The results showed that ammonia was transferred through the gas phase, but also carbonate, which is present in stored urine originating from the hydrolysis of urea. Although the pH in the product stream decreases initially, it rises above pH 7 at longer operation times. This pH increase can be attributed to a combination of proton compensating effects. The use of ammonia-selective membranes for the transfer into the acid concentrate could provide a solution to generate an ammonium phosphate product at low pH and high recoveries.