In this study, a laboratory-scale microfiltration membrane system was operated with olive oil industry wastewater (OMW) and cheese whey effluent (CWE) with chemical oxygen demand (COD) concentrations of 54 and 65.6 g/L at flow rates (Q) of 100, 150, and 200 L/h, pressures of 1 and 2 bar, filtration times considered as four different hydraulic retention time (q) of 30, 60, 90, and 120 min, respectively. COD removal efficiencies decreased with decreasing q from 120 min to 30 min and increasing pressure. In this study, mathematical models such as first-order kinetics, Grau second-order, and Modified Stover-Kincannon models were applied to determine the organic matter removal kinetics of the microfiltration membrane system. The model’s kinetic parameters were determined by linear regression using the experimental data. The predicted effluent COD concentrations were calculated using the kinetic constants. Grau second-order and Modified Stover-Kincannon models were found to be more consistent with the observed data. Moreover, the correlation coefficient (R2) obtained for the experimental and predicted effluent COD concentration also confirmed the suitability of the kinetic models and showed that the models can be used in the kinetics of organic matter removal in microfiltration membrane system design, thus predicting the behavior of the membrane for treating olive oil industry wastewater and cheese whey effluent. The experimental results obtained in this study are expected to be used as a reference for the determination of organic matter removal kinetics in membrane systems.