BACKGROUND: The fate of veterinary antibiotics in manure digesters is of great concern because of poor biomethane recovery and potential development of antibiotic resistant bacteria in the environment. RESULTS: Manure samples collected from therapeutically treated cattle (a standard veterinary practice of 50 mL OTC solution as 20 mg kg(-1) cattle weight) were used in digestion studies. The methane yields of OTC-medicated two-phase and single-phase digesters were 99+/-8 and 72+/-9 mL CH4 g(-1) VS in the presence of 3.11+/-0.12 and 3.07+/-0.14 mg OTC L-1, respectively; whereas, non-medicated two-phase and single-phase digesters had 43% and 52% higher methane yields, respectively. Fluorescence in situ hybridization results indicated that the relative abundance of Firmicutes and Gammaproteobacteria was negatively correlated with the presence of OTC. Methanobacteriales seemed to be a resistant order of methanogenic Archaea to OTC and comparatively higher methane yield in two-phase non-medicated cattle manure digester might be the result of the poor cell activity of Methanosarcinales in two-phase OTC-medicated cattle manure digester. CONCLUSION: Higher OTC removal and biomethane production were achieved by two-phase configuration, thus, it can be an alternative to treat antibiotic-medicatedmanures in full-scale applications in order to reduce its adverse effects. (C) 2015 Society of Chemical Industry