The increasing world population generates huge amounts of wastewater as well as large energy demand. Additionally, fossil fuel’s combustion for energy production causes the emission of greenhouse gases (GHG) and other pollutants. Therefore, there is a strong need to find alternative green approaches for wastewater treatment and energy production. Microalgae biorefineries could represent an effective strategy to mitigate the above problems. Microalgae biorefineries are a sustainable alternative to conventional wastewater treatment processes, as they potentially allow wastewater to be treated at lower costs and with lower energy consumption. Furthermore, they provide an effective means to recover valuable compounds for biofuel production or other applications. This review focuses on the current scenario and future prospects of microalgae biorefineries aimed at combining wastewater treatment with biofuel production. First, the different microalgal cultivation systems are examined, and their main characteristics and limitations are discussed. Then, the technologies available for converting the biomass produced during wastewater treatment into biofuel are critically analyzed. Finally, current challenges and research directions for biofuel production and wastewater treatment through this approach are outlined.