The present invention improves biodiesel production in several ways. Unique combinations of unit operations and flow configurations are disclosed in mobile processing units that are feedstock-flexible and can be dynamically deployed in a distributed way. In some embodiments, a process includes introducing a waste oil and an alcohol into a reactor with an esterification-transesterification enzymatic catalyst. Free fatty acids are reacted with alcohol to produce fatty acid alkyl esters, and glycerides are reacted with alcohol to produce fatty acid alkyl esters and glycerin. A membrane separator removes glycerin, water, and alcohol. Unreacted free fatty acids are then separated and recycled, to generate a product stream with fatty acid alkyl esters. A genset may be provided for combusting glycerin to produce electrical power and thermal heat as co-products. This biodiesel process may be energy self-sufficient, require no external utilities, and avoid direct discharge of wastewater.