Methods and systems for recovering a desired co-product from a feedstock to ethanol production process are provided. The methods involve a multi-step separation of a fermentation-derived feedstock, in which an initial separation produces a discharge stream and an output feed stream including the co-product, and a final separation further purifies the output feed stream while also producing a recycle stream that is reintroduced into the separation process. The systems include at least an initial and at least a final separation device which are in fluid communication in both upstream and downstream directions. The initial separation device separates at least a portion of a non-co-product containing phase from a feed stream comprising the non-co-product containing phase and a co-product containing phase, and the final separation device separates at least a portion of the co-product containing phase from a stream comprising the co-product containing phase and a non-co-product containing phase.