A multi stage process for separating oil, protein, fiber and clean water from a stream containing whole stillage byproduct from ethanol production is disclosed. In a first step, fibers are separated in a two-step process that includes a plate separator and a press. In a subsequent step, the liquid stream separated from the fibers and contains oil, protein and water is treated with a composition that causes the protein to gel. The liquid stream is then processed in a phase separator that drains the oil by gravity, removes the water by an impeller under pressure and removes the solidified protein using a scroll.