An engineering approach was applied to an efficient biodiesel production from waste cooking oil. In this work, an enzymatic packed-bed reactor (PBR) was integrated with a glycerol-separating system and used successfully for methanolysis, yielding a methyl ester content of 94.3% and glycerol removal of 99.7%. In the glycerol-separating system with enhanced retention time, the effluent contained lesser amounts of glycerol and methanol than those in the unmodified system, suggesting its promising ability to remove hydrophilic impurities from the oil layer. The PBR system was also applied to oils with high acid values, in which fatty acids could be esterified and the large amount of water was extracted using the glycerol-separating system. The long-term operation demonstrated the high lipase stability affording less than 0.2% residual triglyceride in 22 batches. Therefore, the PBR system, which facilitates the separation of hydrophilic impurities, is applicable to the enzymatic biodiesel production from waste cooking oil. (C) 2012 Elsevier Ltd. All rights reserved.