Centrate from digested sludge dewatering holds promise for nutrient recovery, but concerns about organic and inorganic contaminants must be addressed. This study investigates the effectiveness of a two-stage system in retaining organic micropollutants, metals, and metalloids during recovery of a multi-nutrient solution from centrate. In combination, the lab-scale membrane bioreactor (MBR) and electrodialysis (ED) effectively reduced contaminant loads by >90% for 21 of the monitored 22 organic micropollutants and for six of nine metals and metalloids. The combined process demonstrated resilience to fluctuations in the MBR stage, with a temporary 87% decrease in MBR removal efficiency for carbamazepine translating to only 6% decrease after the ED. Despite this robust performance, individual compounds such as valsartan acid or benzotriazole were detected at around 10–20 μg L⁻¹ in the recovered nutrient solution. Zn was present at around 400 μg L⁻¹ with the highest concentrations of monitored metals. Still, all metals ranged at least one order of magnitude below recommended values for wastewater reuse. Therefore, the risk associated with contaminant uptake into hydroponically cultivated produce is considered low, given the high retention in the system and the necessary dilution of the multi-nutrient solution before its application as fertilizer. This study demonstrates the effective removal of contaminants by the combination of MBR and ED for nutrient recovery from centrate, achieving a fit-for-purpose quality of the derived multi-nutrient solution.