Anaerobic digestion has emerged as an increasingly popular method for the effective management of organic waste and wastewater with the potential to generate renewable energy. However, efficient digestion depends heavily on the complex and diverse microbial communities mediating this process. This review paper delves into the complex microbiome that exists within anaerobic digestion digesters, playing a critical role in the efficient and sustainable conversion of organic waste into biogas. Its primary focus falls within the scope of how various operational and environmental factors, including temperature, pH, hydraulic retention time, substrate loading rates, and the presence of inhibitory compounds, can substantially impact the microbiome of these systems. Through an extensive analysis of the existing literature, the microbial ecology of anaerobic digestion, including the composition and function of the microbial community, their interactions, and responses to different stressors, are evaluated. By offering critical insights into the distribution patterns of active microbial populations upon alterations in various process parameters, a better understanding of the microbial dynamics within these systems is provided, enhancing their efficiency. Overall, this paper emphasizes the importance of unraveling the microbial evolution within AD reactors to optimize biogas production and sustainable waste management and proposes future perspectives in this direction.