This work presents a superstructure-based optimisation model to optimise the microalgae to biodiesel production flowsheet for the minimum net annualised life cycle cost (ALCC) of biodiesel. The model includes the important processing steps of converting microalgae into biodiesel, viz. microalgae growth, harvesting, lipid extraction, and transesterification of lipid. Different options to perform these steps are considered. The mass and volumetric balance for each process and equipment, and the equipment capacity limitations constitute the important model constraints. The decision variables include growth duration, medium, as well as the techniques and specifications to be followed in each of the downstream steps. The mixed integer linear programming model was applied to a case study of producing 30,000 kg/d biodiesel from Chlorella. The minimum ALCC was US $ 13.286/1 for the flowsheet and equipment details recommended by the model. Sensitivity analysis showed that lipid extraction was the most crucial step in the flowsheet. (C) 2016 Elsevier Ltd. All rights reserved.