Waste treatment and the simultaneous production of energy have gained great interest in the world. In the last decades, scientific efforts have focused largely on improving and developing sustainable bioprocess solutions for energy recovery from challenging waste. Anaerobic digestion (AD) has been developed as a low-cost organic waste treatment technology with a simple setup and relatively limited investment and operating costs. Different technologies such as one-stage and two-stage AD have been developed. The viability and performance of these technologies have been extensively reported, showing the supremacy of two-stage AD in terms of overall energy recovery from biomass under different substrates, temperatures, and pH conditions. However, a comprehensive review of the advantages and disadvantages of these technologies is still lacking. Since microbial ecology is critical to developing successful AD, many studies have shown the structure and dynamics of archaeal and bacterial communities in this type of system. However, the role of Eukarya groups remains largely unknown to date. In this review, we provide a comprehensive review of the role, abundance, dynamics, and structure of archaeal, bacterial, and eukaryal communities during the AD process. The information provided could help researchers to select the adequate operational parameters to obtain the best performance and biogas production results.