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The production of biogas through anaerobic digestion implies the generation of 90–95% of digested raw material, namely digestate. A nutrient-rich stream is generally applied to cropland to enhance yields, due to its high abundance of nutrients. Nevertheless, the intensive digestate farming brings about nutrient saturation and groundwater contamination. The application of downstream emerging technologies that focus on the recovery of nutrients from digestate have been studied, yet freeze concentration technology (FC) has never been considered for this purpose. This study evaluates the performance of FC technology applied to concentrate nitrogen (N), phosphorus (P) and potassium (K) from an effluent of a reverse osmosis unit that is treating the digestate of agro-industrial waste effluents. For this aim, two lab-scale methodological approaches were investigated, namely, progressive FC (PFC) and suspension FC (SFC), set through the utilization of different FC configurations. The concentrates obtained in both FC methods agreed with the regulations for fertilizers in terms of nutrients and metals content; meanwhile, the diluted fraction can be delivered as water for irrigation in high-density livestock areas. The application of FC solves the transportation cost side effect of livestock waste on the one hand, and soil contamination with nutrient on the other hand.