Whole cell lipase catalysis and microalgal feedstocks make overall biodiesel synthesis greener and sustainable. In this study, a novel approach of whole cell lipase-catalyzed conversion of Scenedesmus obliquus lipids was investigated for biodiesel synthesis. Microalgal biodiesel was characterized for its fuel properties. Optimization of process parameters for immobilized Aspergillus niger whole cell lipase-catalyzed biodiesel synthesis was carried out. Highest biodiesel conversion of 53.76% was achieved from S. obliquus lipids at 35 degrees C, methanol to oil ratio of 5:1 and 2.5% water content based on oil weight with 6 BSPs (Biomass support particles). Step-wise methanol addition was applied to account for methanol tolerance, which improved biodiesel conversion upto 80.97% and gave 90.82 +/- 1.43% yield. Immobilized A. niger lipase can be used for 2 batches without significant loss in conversion efficiency. Most of the fuel properties of biodiesel met the specifications set by international standards. (c) 2015 Elsevier Ltd. All rights reserved.