The anaerobic digestion of microalgae is a prospective environmentally feasible option for creating a renewable source of energy for industrial and domestic needs. Microalgae anaerobic digestion is a key unit process that integrates efficiency and beneficially into the production of microalgae derived biofuels. Anaerobic digestion culminating in methane fermentation improves the economic viability of microalgae liquid biofuel production and presents an opportunity for power generation from wastewater derived microalgae. However the anaerobic digestion of microalgae biomass is not straight forward due to several technical restraints including low concentration of digestible biodegradable substrate, recalcitrant substrate constituents, cell wall degradability, low carbon to nitrogen ratio, ammonia toxicity and effects from salinity and associated metal ions. Current production methods for liquid biofuel production from microalgae produce approximately 60–70% residual biomass that is currently a byproduct. Anaerobic digestion provides biogas, but it can also provide essential nutrient recovery from lipid extracted microalgae biomass. The biogas produced from the anaerobic digestion process can be used to generate onsite electrical power or thermal heat to offset biomass processing and extraction processes. When both of these processes are integrated and operated simultaneously, the benefits to microalgae biofuel production and wastewater treatment derived energy production are increased significantly. To consider the integration of anaerobic digestion into a commercial-scale integrated microalgae production and biofuel refinery facility or wastewater treatment plant we present a review of the literature, the current state of the art and future directions for research.