Background <p>Phages shape microbial communities by regulating metabolic pathways, driving biogeochemical processes, and impacting stability and functionality of ecosystems. Phages contributions to natural ecosystems are undeniable; however, their role in built systems especially in anaerobic digesters remain poorly characterized. To discover the functional role of phage communities in anaerobic digesters, we evaluated phage-bacterial and virus-archaeal relationships in metagenomic sequences from fifteen commercial, full-scale anaerobic digesters of chicken, cattle, and pig manure, the three most commonly utilized organic waste streams globally.</p> Results <p>Here, we predict the abundance, auxiliary metabolic genes, and microbial-host interactions of phage and archaeal viruses under anaerobic fermentation processes and methanogenesis. We found phages and prokaryote abundances were coupled and both populations were driven by feedstock characteristics (20% phage variance and 25% prokaryotes explained by feedstock), indicating interactions of phage, host, and the environment. Phages encoded auxiliary metabolic genes relevant to and supporting anaerobic digestion including glycoside hydrolase, pyruvate formate lyase, and cobalamin biosynthesis genes.</p> Conclusions <p>Together, our results reveal that phages are not only integral to bacterial and archaeal community structure and function in anaerobic digesters but are also strongly shaped by feedstock type. These findings provide a basis for understanding and potentially manipulating viral-host interactions to enhance digester performance.</p>