Peristaltic pumping is used in membrane applications where high and sterile sealing is required. However, control is difficult due to the pulsating pump characteristics and the time-varying properties of the system. In this work, three artificial intelligence control strategies (artificial neural networks (ANN), fuzzy logic expert systems, and fuzzy-integrated local models) were used to regulate transmembrane pressure and crossflow velocity in a microfiltration system under high fouling conditions. A pilot plant was used to obtain the necessary data to identify the AI models and to test the controllers. Humic acid was employed as a foulant, and cleaning-in-place with NaOH was used to restore the membrane state. Several starting operating points were studied and setpoint changes were performed to study the plant dynamics under different control strategies. The results showed that the control approaches were able to control the membrane system, but significant differences in the dynamics were observed. The ANN control was able to achieve the specifications but showed poor dynamics. Expert control was fast but showed problems in different working areas. Local models required less data than ANN, achieving high accuracy and robustness. Therefore, the technique to be used will depend on the available information and the application dynamics requirements.