This paper describes the production of struvite by the ion exchange isothermal supersaturation (IXISS) process. By stripping magnesium from a weak cationic resin with ammonium phosphate, a highly supersaturated solution is formed. However, it remains stable while it is flowing along the fixed bed, thus avoiding clogging problems and later facilitating salt separation by self-phase segregation. In this paper, the best ion exchanger for avoiding crystallization inside the column has been selected, and the conditions for stable operation have been investigated. In addition, cyclic fixed bed operation has been checked to evaluate resin performance and long-term operation stability. Eluent concentration mainly modulates the degree of supersaturation during the elution, which is a maximum around the concentration peaks of magnesium. Crystalline aggregates could partially block the ion exchanger surface and stop the ion interdiffusion process. Usually, working with 5–18 mM ammonium phosphate at a specific rate of 7 × 10–5 m3/m2·s, the system can be operated safely and no crystallization occurs inside the bed. The amount of eluted magnesium increases slightly over the operation cycles. After bed stabilization, the operation poses no clogging problems, the performance is reproducible, and the crystallization reactor yields 14 g/h of struvite per kg of dry resin. Consequently, the IXISS process could be applied to the recovery of nutrients from domestic wastewaters.