Oleaginous Scenedesmus sp. was cultivated phototrophically in an open pond for biofuels production. The culture was harvested and subsequently dewatered and dried. The chemical properties of the Scenedesmus sp. lipids were determined as per standard ASTM methods. Biodiesel was synthesized by in situ transesterification from dried biomass using microwave and sonication techniques with tungstated zirconia (WO3/ZrO2) as a solid acid catalyst. In situ transesterification allowed minimizing the requirement of solvents by merging the two steps (i.e. extraction of lipid and conversion to biodiesel) to a single step. The use of a solid catalyst effectively reduces the purification cost of biodiesel due to ease of separation and potential for reuse. The conversion of Scenedesmus sp. lipids to biodiesel was determined by GC. Box-Behnken design was used for optimization of the variables to optimize the biodiesel yield and conversion. The efficiency of the two processes was compared.