A mathematical model was developed for the design of microalgae-based biodiesel production system by systematically integrating all the production stages and strain properties. Through the hypothetical case study, the model suggested the most economical system configuration for the selected microalgae strains from the available processes at each stage, thus resulting in the cheapest biodiesel production cost, S$2.66/kg, which is still higher than the current diesel price (S$1.05/kg). Interestingly, the microalgae strain properties, such as lipid content, effective diameter and productivity, were found to be one of the major factors that significantly affect the production cost as well as system configuration. (C) 2015 Elsevier Ltd. All rights reserved.