Source separation of urine can enable nutrient recycling, facilitate wastewater management, and conserve water. Without stabilization of the urine, urea is quickly hydrolyzed into ammonia and (bi)carbonate, causing nutrient loss, clogging of collection systems, ammonia volatilization, and odor nuisance. In this study, electrochemically induced precipitation and stabilization of fresh urine was successfully demonstrated. By recirculating the urine over the cathodic compartment of an electrochemical cell, the pH was increased due to the production of hydroxyl ions at the cathode. The pH increased to 11−12, decreasing calcium and magnesium concentrations by >80%, and minimizing scaling and clogging during downstream processing. At pH 11, urine could be stabilized for one week, while an increase to pH 12 allowed urine storage without urea hydrolysis for >18 months. By a smart selection of membranes [anion exchange membrane (AEM) with a cation exchange membrane (CEM) or a bipolar membrane (BPM)], no chemical input was required in the electrochemical cell and an acidic stream was produced that can be used to periodically rinse the electrochemical cell and toilet. On-site electrochemical treatment, close to the toilet, is a promising new concept to minimize clogging in collection systems by forcing controlled precipitation and to inhibit urea hydrolysis during storage until further treatment in more centralized nutrient recovery plants.