Systems and methods for using carbon dioxide to remove an alkali catalyst and to recover free carboxylic acids after a transesterification reaction are disclosed. Generally, the methods include first providing a mixture resulting from the transesterification of an ester, wherein the mixture includes substances selected from the alkali catalyst, an alcohol, and a transesterification reaction product such as biodiesel. Second, the methods generally include adding carbon dioxide to the mixture. In some cases, adding the carbon dioxide to the mixture causes the alkali catalyst to convert into an alkali carbonate and/or an alkali bicarbonate. In other cases, adding the carbon dioxide to the mixture causes the carboxylic acid alkali salt to convert into a free carboxylic acid. In either case, the alkali carbonate, the alkali bicarbonate, and/or the free carboxylic acid can be separated from the mixture in any suitable manner.