Methods for controlling a spinning membrane separator so as to limit fouling of the membrane by changing the rotation rate of the spinning membrane in response to the fouling rate, while maintaining a constant outlet cellular concentration. Increasing the spinner rotation rate will increase the strength of the Taylor vortices generated within the separator by the spinning of the membrane, which should reduce fouling of the membrane. The goal of the method is to rotate the spinning membrane at the slowest rate possible without unacceptable fouling. Two specific methods to control fouling are disclosed. In a first, unidirectional method, the spin rate of the membrane is only increased in response to undesirable fouling in order to prevent the fouling from continuing. In a second, bidirectional method, the spin rate of the membrane may be either increased or decreased in response to the measured fouling rate in order to maintain the fouling rate within a desired range.