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.

High-rate algal ponds (HRAP) are cost-effective and viable systems for producing microalgal-bacterial aggregates (MABA) from wastewater, forming a consortium rich in alginate-like exopolymers (ALE) and lipids—raw materials for third-generation biodiesel. However, little is known about the effects of sequencing batch (SB) operation in HRAP. Therefore, the present study evaluated the dynamics of algal genera, sewage treatment, ALE, lipid contents, and biodiesel quality of a pilot HRAP (2400 L) operated in SB over 134 days. After the consortium formation (d0-d20), the pond reached a stability period between days 66 and 128, demonstrating a relative abundance of >80% of Cyclotella sp. and nitrogen, phosphorus, and chemical oxygen demand removals of 90.1 ± 3.7%, 40.1 ± 7.3%, and 66.6% ± 7.6%, respectively. ALE contents reached 87.4 ± 19.3 mg.gTSS-1. The most efficient extraction (Soxhlet+chloroform: methanol 2:1) yielded an average lipid content of 11 ± 2%, with the most abundant methyl esters being C16:0 (35.74%), C18:0 (21.01%), and C16:1 (12.08%). The biodiesel produced met international standards for cetane number, iodine value, kinematic viscosity, and density, while also showing a higher heating value consistent with other renewable energy sources such as soybean. These results imply increased flexibility in the use of HRAP-MABA systems through SB operation and demonstrate the production of high-quality biodiesel from predictable biomass, even under the adverse conditions of open systems.