Methods for the preparation of bio-based malonic acid and diester derivatives of malonic acid are provided. For example, a dialkyl malonate may be prepared by the steps of (i) separating calcium malonate crystals from a fermentation broth; (ii) obtaining dissolved malonic acid; (iii) crystallizing the dissolved malonic acid; and (iv) performing esterification to obtain the dialkyl malonate. The disclosed methods produce diester derivatives of malonic acid with fewer impurities, which is useful for many industrial processes. The diester derivatives of malonic acid can be purified from existing sources of malonic acid, or from malonic acid made from a renewable carbon source.