It is reported for the first time, the selection of an industrial centrifuge with the optimized geometry and operational conditions to efficiently separate the diphtheria bacterial cell debris from the culture medium and particularly to harvest the purified bacterial toxin by using the computational fluid dynamics (CFD) simulation and experimental approaches. The industrial-scale tubular and disc stack centrifuges each with two different sizes were first simulated to quantify their complex hydrodynamics. An optimal balance among the rotational speed, feed flow rate, and possible cell damages was required to efficiently separate the bacterial cells. It was also revealed that both large-sized tubular and disc stack centrifuges perform remarkably better than the smaller ones. Ultimately, according to the CFD simulation results, among four centrifuges, the large-sized disc stack centrifuge with the rotational speeds upper than 5500 rpm and the feed flow rates lower than 100 L h−1 was a potential candidate to utilize in the real process. Through performing experiments by using an industrial disc stack centrifuge, a good agreement was found between the CFD and experimental data in terms of the optimized rotational speed and feed flow rate required for the separation of cells. The Ramon flocculation assay confirmed the preserved quality and quantity of the main product of this bioseparation process, ‘the bacterial toxin purified from the bacterial cell debris’.