According to the European Standard EN 14214, biodiesel fuels must have significant purity values; therefore, a post transesterification purification process is required to produce the fuel that fulfills the standard. Until recently, water washing was conventionally preferred as a biodiesel purification method. In this study, upon completion of the two parallel transesterification reactions, one of the reaction mixtures was washed with water and the other one with polyethylene glycol 300 (PEG 300), a flocculation agent, under several concentration conditions in order to compare two different purification methods, and which of them obtains better results. The features of biodiesel washed with PEG 300 were found to be similar to those of the other. Moreover, washing with PEG 300 was found to provide less glycerol precipitation time than conventional glycerol decantation. This process provided easy production of fatty acid alkyl esters without acid neutralization and deionized water-washing procedures that were necessary to produce a high-purity product onto the conventional transesterification process. The new washing process enabled low-cost production of the biodiesel from refined vegetables.