Although microalgae represent a promising alternative feedstock for biofuels, the current solvent-based lipid conversion systems and processes are neither cost-effective nor energy-efficient due to the bad quality of algal crude lipids. In the present study, a novel lipase-catalyzed transesterification method with crude Chlorella lipids was systematically investigated and optimized. A highly efficient conversion protocol with 97% of fatty acid methyl esters (FAME) yield was obtained after the introduction of co-solvent. Then several crucial parameters including the reaction time, molar ratio of algae oils to methanol, ratio of algae oils to co-solvent, ratio of algae oils to lipase and reaction temperature and intensively studied and selected at 12 h, 1: 12, 1: 1 (m/v), 20: 1 (m/m) and 40 degrees C, respectively. In addition, the reusability of the immobilized lipase was also investigated with crude algal lipids. The immobilized lipase could maintain 84% of its original activities even after five recycles. Polar lipid standards along with the polar lipids isolated from crude algal lipids were also tested and results indicated that they could also be converted into biodiesel very efficiently. This study provides an important insight into further decreasing the downstream processing costs in algae-based biofuel production. (C) 2017 Elsevier Ltd. All rights reserved.