Using biological processes to treat soybean wastewater has great potential, because it generates biomass and reduces sludge production. The formation of Aspergillus niger pellets during cultivation in wastewater has the additional benefit that such pellets are easy to harvest. In the first wastewater treatment step, A. niger pelletization decreased the chemical oxygen demand (COD) by 80.35%. In the second step, A. niger, when combined with added nutrients and cultivated in the presence of Pichia pastoris, did not decrease the COD. Aspergillus niger did not degrade some carbon compounds according to total carbon, organic carbon, and inorganic carbon analysis. The COD decreased from 3.26 £ 10 4 mg O 2 /L to 616.67 mg O 2 /L (a 98.11% COD reduction) after activated carbon absorption, which indicates that this approach is efficient. In summary, this study proposes a combined method to treat high-COD-value soybean wastewater.