This paper provides an analysis of the potential environmental impacts of biodiesel production from microalgae. High production yields of microalgae have called forth interest of economic and scientific actors but it is still unclear whether the production of biodiesel is environmentally interesting and which transformation steps need further adjustment and optimization. A comparative LCA study of a virtual facility has been undertaken to assess the energetic balance and the potential environmental impacts of the whole process chain, from the biomass production to the biodiesel combustion. Two different culture conditions, nominal fertilizing or nitrogen starvation, as well as two different extraction options, dry or wet extraction, have been tested. The best scenario has been compared to first generation biodiesel and oil diesel. The outcome confirms the potential of microalgae as an energy source but highlights the imperative necessity of decreasing the energy and fertilizer consumption. Therefore control of nitrogen stress during the culture and optimization of wet extraction seem to be valuable options. This study also emphasizes the potential of anaerobic digestion of oilcakes as a way to reduce external energy demand and to recycle a part of the mineral fertilizers.