Human urine is a valuable resource for nutrient recovery, given its high levels of nitrogen, phosphorus and potassium, but the compositional complexity of urine presents a challenge for an energy-efficient concentration and refinery of nutrients. In this study, a pilot installation combining precipitation, nitrification and electrodialysis (ED), designed for one person equivalent (1.2 L_urine d⁻¹), was continuously operated for ∼7 months. First, NaOH addition yielded calcium and magnesium precipitation, preventing scaling in ED. Second, a moving bed biofilm reactor oxidized organics, preventing downstream biofouling, and yielded complete nitrification on diluted urine (20–40%, i.e. dilution factors 5 and 2.5) at an average loading rate of 215 mg N L⁻¹ d⁻¹. Batch tests demonstrated the halotolerance of the nitrifying community, with nitrification rates not affected up to an electrical conductivity of 40 mS cm⁻¹ and gradually decreasing, yet ongoing, activity up to 96 mS cm⁻¹ at 18% of the maximum rate. Next-generation 16S rRNA gene amplicon sequencing revealed that switching from a synthetic influent to real urine induced a profound shift in microbial community and that the AOB community was dominated by halophilic species closely related to Nitrosomonas aestuarii and Nitrosomonas marina. Third, nitrate, phosphate and potassium in the filtered (0.1 μm) bioreactor effluent were concentrated by factors 4.3, 2.6 and 4.6, respectively, with ED. Doubling the urine concentration from 20% to 40% further increased the ED recovery efficiency by ∼10%. Batch experiments at pH 6, 7 and 8 indicated a more efficient phosphate transport to the concentrate at pH 7. The newly proposed three-stage strategy opens up opportunities for energy- and chemical-efficient nutrient recovery from urine. Precipitation and nitrification enabled the long-term continuous operation of ED on fresh urine requiring minimal maintenance, which has, to the best of our knowledge, never been achieved before.