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Traditional activated-sludge treatment technologies, such as anaerobic/anoxic/aerobic processes, oxidation ditch processes, and sequential batch reactors, play a crucial role in the removal of nitrogen and phosphorus from municipal wastewater. The synergistic interactions among functional microorganisms, primarily nitrogen-removal organisms and phosphorus-accumulating organisms, are paramount in these processes. However, traditional activated sludge treatment technology consumes large amounts of energy and produces a substantial volume of waste-activated sludge, necessitating the upgrade of municipal wastewater treatment plants (WWTPs) focusing on sustainable development goals. This review analyzes and characterizes key functional microorganisms (Nitrosomonas, Nitrosospira, Nitrobacter, Nitrospira, Thauera, Pseudomonas, Candidatus Brocadia, Candidatus Kuenenia,and Candidatus Accumulibacter) involved in nitrogen and phosphorus removal in municipal wastewater treatment. It also explores the impact of operating conditions, influent quality, and reactor configurations on the synergistic regulation of these functional microorganisms for efficient nutrient removal, with emphasis on upgrading and reconstructing traditional nitrogen-removal techniques and full-scale anaerobic ammonium oxidation (anammox) processes. Integrated fixed-film activated sludge-based (IFAS), aerobic granular sludge-based (AGS), and moving bed biofilm reactor (MBBR) technologies are promising to enhance and transform the conventional processes, realizing new engineering applications and sustainable practices. Other promising developments are the use of heterotrophic denitrifying bacteria such as Thaueraand anammox bacteria (Candidatus Brocadiaand Candidatus Kuenenia) for mainstream partial denitrification/anammox processes, which are potentially expandable to full-scale municipal WWTPs.