Ammonia and phosphate, which are present in large quantities in waste streams such as livestock manure, are key compounds in fertilization activities. Their recovery will help close natural cycles and take a step forward in the framework of a circular economy. In this work, a lab-scale three-chambered microbial electrolysis cell (MEC) has been operated in continuous mode for the recovery of ammonia and phosphate from digested pig slurry in order to obtain a nutrient concentrated solution as a potential source of fertilizer (struvite). The maximum average removal efficiencies for ammonium and phosphate were 20% ± 4% and 36% ± 10%, respectively. The pH of the recovered solution was below 7, avoiding salt precipitation in the reactor. According to Visual MINTEQ software modelling, an increase of pH value to 8 outside the reactor would be enough to recover most of the potential struvite (0.21 mmol L−1 d−1), while the addition of up to 0.2 mM of magnesium to the nutrient recovered solution would enhance struvite production from 5.6 to 17.7 mM. The application of three-chambered MECs to the recovery of nutrients from high strength wastewater is a promising technology to avoid ammonia production through industrial processes or phosphate mineral extraction and close nutrient natural cycles.