This work investigated the individual and combined effects of zinc oxide, norfloxacin, and sulfamethazine on sludge anaerobic digestion-associated methane production, protein and carbohydrate metabolism, and microbial diversity. Norfloxacin and sulfamethazine (500 mg/kg) did not inhibit methane production, but inhibited its production rate. Zinc oxide nanoparticles with antibiotics inhibited hydrolysis, fermentation, and methanogenesis over varying digestion periods. Complex pollution had a greater impact on methane production than zinc oxide alone, with acute, synergistic toxicity to methanogenesis over short periods. Complex pollution also had varying effects on bacterial and archaeal communities during digestion. These results aid understanding of the toxicity of emerging contaminants in sludge digestion, with the potential to improve pollution removal and reduce associated risks.