The removal of emerging pollutants from sewage waste has emerged as a pressing global challenge due to their adverse effects on both human health and the environment. Microbial-based systems have garnered significant attention as sustainable and effective approaches for mitigating emerging pollutant contamination. This chapter provides a comprehensive overview of microbial-based systems for the removal of emerging pollutants from sewage waste, addressing the pressing global challenge of mitigating their adverse impacts on human health and the environment. It examines the key emerging pollutants present in sewage waste, their sources, and the mechanisms through which microbial communities can degrade, transform, or immobilize these contaminants. Various microbial-based treatment technologies, including activated sludge processes, biofilm reactors, constructed wetlands, and microbial fuel cells, are critically evaluated for their efficacy in pollutant removal. Factors influencing system performance, such as microbial community composition, environmental conditions, and operational parameters, are discussed alongside recent advances in microbial ecology and biotechnology that enhance treatment efficiency. Challenges and limitations are addressed, with strategies for optimization and overcoming obstacles presented, including bioaugmentation and integration with physicochemical processes. The chapter concludes by highlighting prospects and emerging trends, emphasizing the need for interdisciplinary collaboration to advance microbial-based technologies toward sustainable wastewater treatment and environmental protection.