The optimization of wastewater treatment technologies using biological processes is no longer limited to improving the removal of organic matter and nutrients, as it is possible to reduce area and energy consumption, and recover value-added by-products. In this context, the microalgae–bacteria consortium is an alternative for reducing costs, as microalgae produce the oxygen required by bacteria to oxidize organic matter through photosynthesis. Additionally, it is possible to extract different by-products such as lipids, biofertilizers, biogas, alginate-type exopolymers, and others. Furthermore, bioflocculation occurs naturally through the adhesion of microalgae to the surface of bacterial flocs, without the addition of chemical products. This review discusses the main systems that utilize the microalgae–bacteria consortium, the metabolism of the microalgae–bacteria consortium, and its performance in removing organic matter and nutrients, as well as the effect of operating conditions on the physical properties of the biomass. Among the highlighted systems are sequencing batch and single-batch reactors, high-rate ponds, and continuous flow reactors. Among the systems discussed in this work, the sequential batch reactor configurations found better biomass formation and production of extracellular polymeric substances and the continuous flow reactors showed lower installation and operating costs. From this perspective, the potential for full-scale application of each system can be evaluated once the optimum operating conditions have been defined and the limitations of each system have been understood.