This paper deals with a multi-objective optimization of a general batch diafiltration process in the presence of fouling. Fouling, as one of the major problems in the membrane separation process, causes the decrease in the membrane area and thus the decrease in the filtration rate. The optimization problem considers a weighted combination of objectives for minimum-time and minimum-diluant operation. We apply numerical (orthogonal collocation) and analytical (Pontryagins minimum principle) methods to obtain the optimal operation of diafiltration process when fouling is considered. A case study from literature highlights the properties and economical benefits of the optimal operation.