Carboxylic acids are common products produced from the bioconversion of renewable feedstocks. In these processes the separation of the acid product from fermentation broth is the most energy and cost intensive unit operation. Thus, the development of robust, scalable separation approaches that can be applied to a variety of carboxylates is of critical importance to the development of processes that utilize carboxylic acids as platform chemicals. Here we report a batch separation method that includes cell and particulate removal, cation exchange, activated carbon treatment, dewatering with a polymer resin, and product recovery. This method is demonstrated on two unique fermentation broths both derived from corn stover hydrolysate to separate neat succinic and propionic acid. For succinic acid, a crystallization yield of 91% with a product purity of 99.93% was achieved. To our knowledge this is the highest reported crystallization yield and purity for the recovery of succinic acid. Additionally, the method requires approximately 50% less energy compared to standard evaporative crystallization approaches. For propionic acid, neat liquid product was obtained with a distillation yield of 80% and purity of 98%. Finally, these excellent results achieved in terms of yield and purity for succinic and propionic acid, two acids with widely different physical properties, from chemically complex hydrolysate broth demonstrates the effective and robust nature of this approach.