This chapter describes the enzymatic biodiesel production via transesterification of vegetable oils. New original experimental data show that vegetable oils with high fatty acid contents can be directly processed to produce biodiesel with enzymes. Another pathway is also proposed where a biodiesel is produced in coproduction with monoglycerides and diglycerides. These MG/DG/alkylesters can be separated via liquid–liquid extraction. It can be concluded that liquid–liquid extraction can effectively extract MG from glycerolysis and partial alcoholysis products. As high as 80 wt% MG can be obtained after extraction. The authors think that the combination of biodiesel production and MG/DG as a coproduct provides more economic possibilities for performing the enzymatic biodiesel production process. A literature review shows that there is general consensus in the studies that the enzymatic production of biodiesel is a superior method as compared to conventional chemical transesterification, considering the lower complexity of the reaction process and the absence of waste products, in particular glycerin and soap (produced due to the presence of free fatty acids in the waste oil), which will create environmental problems if disposal is not handled appropriately. Reuse of the enzymes is essential for the economy of the process. A method for enzyme reuse is tested and described.