The paper reports on the implementation and the design of a controller for a fuel cell blower (FCB) with active magnetic bearings (AMBs). The cascaded position-fluxcentralized controller is comprised of a centralized position control loop and an inner flux control loop. The last one is based on state estimation without explicit flux measurements. As the position control is not dependent on the magnetic field nonlinearities, such a control structure enables operation under a zero bias. The practical working implementation of a flux control for the industrial levitated rotor is shown for the first time. The flux control gives better results than current control for both normal and zero bias operation. The system is analyzed fully, combining rotor dynamics and power amplifier analyses simultaneously. The importance of using the coil voltage in addition to current and practical treatment of the flux control is revealed. The centralized position-flux controller is compared with a state-of-the-art cascaded position-current control, which has inner current control loops. The proposed control solution with a zero bias can achieve a dynamic performance comparable that of a controller with the classical bias current.