Microalgae-based wastewater treatment has been conceived to obtain reclaimed water and produce microalgal biomass for bio-based products and biofuels generation. However, microalgal biomass harvesting is challenging and expensive, hence one of the main bottlenecks for full-scale implementation. Finding an integrated approach that covers concepts of engineering, green chemistry and the application of microbial anabolism driven towards the harvesting processes, is mandatory for the widespread establishment of full-scale microalgae wastewater treatment plants. By using nature-based substances and applying concepts of chemical functionalization in already established harvesting methods, the costs of harvesting processes could be reduced while preventing microalgae biomass contamination. Moreover, microalgae produced during wastewater treatment have unique culture characteristics, such as the consortia, which are primarily composed of microalgae and bacteria, that should be accounted for prior to downstream processing. The aim of this review is to examine recent advances in microalgal biomass harvesting and recovery in wastewater treatment systems, considering the impact of consortia variability. The costs of available harvesting technologies, such as coagulation/flocculation, coupled to sedimentation and differential air flotation, are provided. Additionally, promising technologies are discussed, including autoflocculation, bioflocculation, new filtration materials, nanotechnology, microfluidic and magnetic methods.