New regulations in environment protection and increasing market demands for “green” companies are forcing the industry to consider finding new and sustainable methods of wastewater treatment. The valuable information regarding treatment of the wastewater from the edible oil industry is presented in this research. The obtained results confirm a promising application of the third generation membranes, comprised of ceramic material (aluminium oxide), in treatment of wastewater from the edible oil industry. Positive results regarding chemical oxygen demand reduction and turbidity removal were noticed. Permeate flux values were used for process optimization in order to achieve a cost-effective process. Response surface methodology was used for the experimental design. The effects of wastewater temperature, transmembrane pressure, and feed-flow rate on the microfiltration model fit were studied. The experiments showed that microfiltration of this type of wastewater is a convenient technique for a possible large scale industrial application as a secondary step in treating wastewater from the oilseed processing facilities.