This chapter explores the efficiency of a waste treatment and its associated flue gas cleaning process was investigated by doing a mass balance of the main species present in the fumes of an industrial waste incineration plant. The first flue gas cleaning process installed on the plant consisted in a neutralisation of acid gases by duct injection of dry sodium bicarbonate with subsequent filtration on ceramic filters, followed by a Selective Catalytic Reduction of nitrogen oxides by urea. A meat and bone meal and sewage sludge co-incineration plant gas cleaning system was investigated, two ceramic filtrations systems, catalytic and non catalytic, were compared by a mass balance of main chemical species. A good efficiency of the gas cleaning was observed despite the high quantity of gas emitted due to the important concentrations of S, Cl and mostly N in the wastes mixture.