Microalgae-based biodiesel has several benefits over other resources such as less land use, potential cultivation in non-fertile locations, faster growth and especially a high lipid-to-biodiesel yield. Nevertheless, the environmental and economic behavior for high scale production depends on several variables that must be addressed in the scale-up procedure. In this sense, rigorous modeling and multicriteria evaluation are performed in order to achieve optimal topology for third generation biodiesel production. Different scenarios and the most promising technologies tested at pilot scale are assessed. Besides, the sensitivity analysis allows the detection of key operating variables and assumptions that have a direct effect on the lipid content. The deviation of these variables may lead to an erroneous estimation of the scale-up performance of the technology reviewed in the microalgae-based biodiesel process. The modeling and evaluation of different scenarios of the harvesting, oil extraction and transesterification help to identify greener and cheaper alternatives.