Biodiesel as alternative for conventional diesel fuel is mainly produced by the catalytic reaction of triglycerides with an alcohol. In this work, the purification of biodiesel was carried out with two lab-made solvent-resistant composite nanofiltration membranes of poly(vinylidene difluoride) (PVDF) as support and poly(dimethylsiloxane) as coating layer. Biodiesel was obtained from the esterification of partially refined soy oil with bioethanol (EtOH) and NaOH as catalyst. The best biodiesel purification performance was achieved with the PVDF-12SI membrane reaching high retention of glycerol, total glycerides, and soap. PVDF-SI membranes were found to have an excellent stability for biodiesel permeation, achieving a flux recovery ratio of EtOH as high as 0.94 after twenty cycles of use.