Abstract Biodiesel from microalgae is regarded as a green and renewable energy source; it is produced from non-food feedstock material, has a high quantity of free fatty acids per unit weight of dry matter, may be cultivated with relatively low land use requirements, and may be adapted to regions with growing economies. Nevertheless, microalgal-based biodiesel production systems are still far from being exploitable on a commercial level due to high energy and resource requirements associated with the lipid extraction processes. Microalgae growth requires significant quantities of water, and the extraction of lipids involves the use of solvents, typically polar/non-polar co-solvent systems. Together, these factors affect the overall efficiency of the conversion process and, thus, the overall environmental and economic footprint, as measured through a life cycle assessment approach. One proposed option to improve the overall efficiency of the process is to substitute the traditional chloroform/methanol-based extraction process with a greener and more novel type of lipid extraction technology such as CO 2 expanded methanol, using a flow-through reactor (CXM). Through the development of an LCA model the current study aims to compare biodiesel production respectively using a conventional organic co-solvent-based extraction system (CHCl 3 – MeOH), a non-expanded methanol in a flow-through reactor (NCXM), and the proposed CXM approach. The comparison, based on three different LCA models, will provide an insight of the effects of the different energy performances of both CXM and NCXM lipid extractions respect to the conventional approach in terms of environmental impacts associated with one unit of biodiesel production. In the long term, the results will be used to identify the environmental ‘hot-spots’ associated with each process, and to explore the potential for improving novel CXM processes.