During downstream processing, it may sometimes be more favorable to use adsorbents to bind the contaminants rather than the product. This so-called flow-through mode is especially useful for feed streams where contaminants are in low concentrations, because less adsorbent is required than for binding large amounts of product. It can also be especially interesting if obtaining a high product yield is secondary to other considerations. For example if an excess of a low value waste stream is available, it may be acceptable that some target is lost to the adsorbent during contaminant binding. However under such unusual conditions, new options for downstream processing are necessary such as Continuous Magnetic Extraction. The application of Continuous Magnetic Extraction in flow-through mode is demonstrated with soy whey as an example feed stream. The target molecule was the Bowman-Birk protease inhibitor which has an anti-carcinogenic effect. It was found that using anion exchange magnetic particles as the impurity adsorbing agent, Continuous Magnetic Extraction of contaminants led to a BBI preparation with purity approaching 97% and with yield of 55% in a 15 L pilot scale system. (C) 2014 Elsevier B.V. All rights reserved.