The present invention generally relates to a novel process in which thin stillage is processed to produce algae oil and protein rich biomass as well as other energy rich byproducts. In accordance with a preferred embodiment, thin stillage is removed from an evaporator during the evaporation process to produce mid-stillage. This mid-stillage is preferably routed to a new process where it is directed to a pre-treatment centrifuge to remove suspended solids, sludge and corn oil. Thereafter, the mid-stillage is preferably cooled and then directed to a fermentation tank where the mid-stillage is subject to a batch fermentation process with algae “seed” fed from an algae inoculation system. Once the batch is harvested, the oil-rich algae/mid-stillage is then preferably heated to rupture the cells and liberate the oil. Thereafter, the oil-rich algae/mid-stillage is preferably processed by a centrifuge which produces solids, a light phase oil and a “clean” mid-stillage stream that can be evaporated to a very high level of solids.