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 􀀀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. ; Copyright: 2016. Elsevier. Due to copyright restrictions, only the abstract is available. For access to the full text item, please consult the publisher's website. The definitive version of the work is published in Renewable Energy, Vol 8. Pp 1002-1010. http://www.sciencedirect.com/science/article/pii/S0960148115301543