High-gradient magnetic filtration bases on the separation of target media by synthetic particles with magnetic core and an adsorbent immobilized on the surface. The process was used in a pilot line at liter-scale for the separation of a protein Bowman-Birk protease Inhibitor (BBI) out of an industrial coproduct stream in the soy industry. The target protein has potential applications as pharmaceutical or food additive. The starting medium is challenging as the product cost is low, its concentration is low and its purity needs to be high. The main method tested was magnetically enhanced centrifugation in a batch-wise mode with anion exchange ligands. The separation of the target protein at large scale was successful and economical. The efficiency was low due to the low ligand selectivity and the batch-wise processing. For commercialization, high ligand selectivity and continuous processing would make this new magnetic separation process very attractive. An economic study was performed to determine the influence of different parameters on prices. Competing technologies were evaluated. A risk analysis of nanoparticles used in the pilot ... mehr line was performed.