Algae are an attractive biofuel feedstock because of their fast growth rates and improved land use efficiency when compared with terrestrial crops. Process train components needed to produce algal biofuels include (1) cultivation, (2) harvesting, and (3) conversion into usable fuel. This paper compares various process train options and identifies knowledge gaps presently restricting the production of algal biodiesel and algae-derived biogas. This analysis identified energy-intensive processing and the inability to cultivate large quantities of lipid-rich algal biomass as major obstacles inhibiting algal biodiesel production. Anaerobic digestion of algal biomass requires fewer process train components and occurs regardless of lipid content. In either scenario, the use of wastewater effluent as a cultivation medium seems necessary to reduce greenhouse gas emissions and maximize water use efficiency. Furthermore, anaerobically digesting algal biomass generated from low-technology wastewater treatment processes represents an appropriate technology approach to algal biofuels that is poorly investigated. Coupling these processes can improve global health by improving sanitation, while providing a cleaner burning biogas alternative to indoor biomass cooking systems typical of less-developed areas.