This paper presents an initial investigation on controller tuning with the effect on membrane fouling in submerged membrane bioreactor (SMBR). This work employed proportional integral derivative (PID) controller to control SMBR filtration process. The PID controller is tuned using three different methods which are Ziegler Nichols (ZN), Cohen Coon (CC) and integral time-weight absolute error (ITAE) tuning. The PID controller is used to control the SMBR filtration permeate flux. Transmembrane pressure (TMP) was observed during the filtration process that will determine fouling effect on controller tuning. The simulation work is done using artificial neural network (ANN) model that was developed in our previous work. Different set points were tested to see the robustness of the controller tuning. The overall result shows the ITAE tuning method performs better compare with other tuning methods in term of its overshoot, settling time and integral absolute error (IAE) with 0.66%, 9.1 second and 82.68 respectively. This tuning method provides precise control performance in the same time it will prevent from decrement of flux in the filtration cycle.