A system and method of anaerobically digesting ethanol stillage and reintegrating substantially all by-products thereof back into the system is disclosed. The system includes an ethanol producing facility for producing ethanol and an anaerobic digestion facility for anaerobically digesting stillage from the ethanol producing facility to produce a plurality of by-products. A plurality of sub-systems utilize the plurality of by-products from anaerobic digestion to produce a plurality of end-products. At least one of the plurality of end-products from the various sub-systems is integrated back into the ethanol producing facility and into at least one of the sub-systems such that the system of anaerobically digesting stillage is a continuous and self-sustaining operation.