Abstract: The production of fatty acid alkyl esters in a refinery setting is broken into three sections which comprise of: the preprocessing high FFA feedstocks; the transesterification of feedstock into fatty acid alkyl esters and; the purification of the fatty acid alkyl esters. Within each of these sections of the refinery, a system of controls and an on-line, real time series of tests utilizing pH, conductivity, viscosity, near infra red spectroscopy, gas chromatography water content and flash point are utilized to tell a process controller when the product is acceptable to move to the next stage of processing.