Microalgae oil has been identified as a reliable resource for biodiesel production due to its high lipid productivity and potential cultivation in non-fertile locations. However, high scale production of microalgae based biodiesel depends on the optimization of the entire process to be economically feasible. The selected strain, medium, harvesting methods, etc., sorely affects the ash content in the dry biomass which have a direct effect in the lipid content. Moreover, the suitable lipids for biodiesel production, some of the neutral/saponifiable, are only a fraction of the total ones (around 30% dry base biomass in the best case). The present work uses computational tools for the modeling of different scenarios of the harvesting, oil extraction and transesterification. This rigorous modeling approach detects process bottlenecks that could have led to an overestimation of the potentiality of the microalgae lipids as a resource for the biodiesel production. (C) 2013 Elsevier Ltd. All rights reserved.