Aspergillus niger biomass, an industrial by-product of citric acid fermentation is an emergent source of glycoderivatives with applications in biofuel, cosmetics, feed, energy, food, medicine, and nanotechnology. In this study, the effect of purified neutral protease for deprotenization of fungal biomass studied at various levels (0, 5, 10, 20 and 40 U/100 mg of biomass) and the saccharification of fungal biomass was evaluated with amylolytic enzymes and chitosanases. The efficiency of deproteinization of fungal biomass was based on the enzyme concentration and contact time. Protease at a concentration of 20 U/100 mg of dry biomass and with a contact time of 8 h achieved 30% final deproteinization. No effect on saccharification of A. niger biomass was observed by treatment with purified amylolytic enzymes. Meanwhile, the endo- and exo-chitosanases treatment yielded 54 g of g reducing sugars (equivalent to amino sugars)/ kg of fungal biomass, which can be employed for tailor-made carbohydrate production.