In the study presented we aim at demonstrating the feasibility of expanding the three phase bioreactor concept to FAAE production from microalgae lipids extracted from two different well kwon strains for biodiesel production, i.e. the fresh water microalgae Botryococcus braunii and the marine microalgae Nannochloropsis gaditana. The main process parameters of the system such as temperature,and alcohol to lipid ratio were evaluated in a broad range to provide useful information towards the scaling up of the operation. The effect of the type of acyl acceptor, surface area and nutrient availability in the performance of the WCTB was evaluated.