A process for making a hydrogenated product includes providing a clarified DAS-containing fermentation broth, distilling the broth to form an overhead that includes water and ammonia, and a liquid bottoms that includes MAS, at least some DAS, and at least about 20 wt% water, cooling and/or evaporating the bottoms, and optionally adding an antisolvent to the bottoms, to attain a temperature and composition sufficient to cause the bottoms to separate into a DAS-containing liquid portion and a MAS-containing solid portion that is substantially free of DAS, separating the solid portion from the liquid portion, recovering the solid portion, hydrogenating the second solid portion in the presence of at least one hydrogenation catalyst to produce the hydrogenated product comprising at least one of THF, GBL or BDO, and recovering the hydrogenated product.