Sulfite ions are by-products in different industrial processes. As they are highly toxic the way for their disposal is to oxidize them to harmless sulfates that can be commercially useful product such as building gypsum or fertilizers. The oxidation process used up to now is an expensive and energy consuming one. The present study is an attempt for their removal with energy generation at the same time in a fuel cell of our design. In our previous papers, we have shown the process of optimization of the design of the cell and the electrodes. This paper shows the process of optimization of the operating conditions by the choice of membranes, initial concentrations, electrolyte content and pH.