High-gradient magnetic separation (HGMS) allows solid/solid/liquid separation in one step and can therefore be used as first capture step in downstream processing of biotechnology products. Magnetic beads are retained in the filter compartment while biomass, solvent and dissolved substances should pass the magnetic filter unhindered. During magnetic filtration agglomeration areas of magnetic beads continuously build up and it is possible that the biomass drags with it some magnetic beads and hence a part of the sorbed product as well. For proper in-process operation of a HGMS filter, it is necessary to measure the concentration of the magnetic beads in the suspension at the outlet of the filter. A novel measurement technique using a flow-through magnetic sensor was developed which allows quantifying the magnetic beads in flowing suspensions.