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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., The authors would like to thank the support provided by two distinct projects: Cyan2Bio (funded by the Spanish Ministry of Science and Innovation (MCIN), the Research National Agency (AEI), and the European Regional Development Fund (FEDER) under the grant agreement PID2021-126564OB-C32) and PROMICON (funded by the European Union’s Horizon 2020 research and innovation programme under the grant agreement No 101000733). The knowledge derived from these projects has been instrumental in enriching the depth of this article. Enrica Uggetti is grateful to the Spanish Ministry of Industry and Economy for her research grant (RYC2018-025514-I). Igor C.F. Sampaio is grateful to the Brazilian National Council for Scientific and Technological Development (CNPq) for the financial support and his postdoctoral scholarship (Call 26/2021). Eva Gonzalez-Flo is grateful to the European Union-Next Generation EU, Ministry of Universities and Recovery, Transformation and Resilience Plan for her research grant [2021UPF-MS-12]. Joan Garcia acknowledges the support provided by the ICREA Academia program., Peer Reviewed, Objectius de Desenvolupament Sostenible::6 - Aigua Neta i Sanejament, Postprint (published version)