The growing market of biopharmaceuticals and the constant developments in upstream fermentation have generated a strong demand for new downstream purification methods. Magnetic separation in combination with functional magnetic particles has been known for many years as a promising candidate for a direct capturing tool in protein purification but the lack of suitable GMP-compliant purification equipment has prevented the launch of this technology in large scale bioprocessing. To tackle this bottle-neck, the principle of a "rotor-stator" high-gradient magnetic separator is fully redesigned to meet the rigorous requirements of modern cGMP biotechnology purification processes. In order to fulfill regulatory requirements, the separation chamber is reengineered to allow effective cleaning and sterilization in place while maintaining excellent separation capacities and efficiencies. Two kinds of commercially available magnetic particles are used to validate key performance data and determine system related parameters in order to calculate process performance figures for process optimization of the new magnetic separation device. With separation capacities of over 400 g of magnetic particles per liter of separation chamber volume and separation efficiencies as well as recovery rates over 99%, the system is able to process more than 200 l crude feedstock per day and capture more than 1.6 kg target compounds.