Abstract: Systems and methods for improving stillage are disclosed. Stillage may include either whole stillage or thin stillage. The system includes taking the stillage and placing it within a bioreactor with an inoculation of fungi. The fungi may include any of Aspergillus niger, Phanerochaete chrysosporium and Yarrowia lipolytica. The fungi and stillage broth is then subjected to fermentation which removes solubles and particulates from the stillage. The fungi generate a biomass material that may be collected and dried for use as a nutritional supplement or other purpose. The remaining liquid is a clarified, treated stillage suitable for a variety of downstream applications, including being used as a backset in an ethanol production facility.