The influence of magnetite nanoparticles, granular activated carbon (GAC), and biochar, as well as their combinations on the anaerobic digestion of chicken manure and the structure of microbial communities was studied. The addition of magnetite, GAC, and biochar increased the rate of methane production and the total methane yield. It has been observed that these additives stimulated anaerobic microorganisms to reduce the concentration of accumulated volatile organic acids. Various bacterial species within the classes Bacteroidia and Clostridia were found at higher levels in the anaerobic reactors but in different proportions depending on the experiment. Members of the genera Methanosarcina, Methanobacterium, Methanothrix, and Methanoculleus were mainly detected within the archaeal communities in the anaerobic reactors. Compared to the 16S rRNA gene-based study, the mcrA gene approach allowed a higher level of Methanosarcina in the system with GAC + magnetite to be detected. Based on our findings, the combined use of granular activated carbon and magnetite at appropriate dosages will improve biomethane production.