Favorable growth characteristics continue to generate interest in using triacylglycerides (TAGs) produced from microalgae for biodiesel feedstocks. In this opinion article, we suggest that due to the energy consumption associated with the production of external nitrogen fertilizers, the manner in which nitrogen is supplied to microalgae biorefineries will be an important driver of energy yields, sustainability, and commercial success. Schemes including the reuse of urban wastewater represent improvements on the overall energy balance, but will not allow for significant production of biofuels unless the nitrogen from the non-TAG portions of microalgae is recycled. Approaches to recycling nitrogen require an improved understanding of the tradeoffs between the different potential uses of the non-TAG microalgal portion (i.e., energy production via anaerobic digestion or thermal catalytic processes), and the development of nitrogen separation technologies.