Antibiotic-resistant microorganisms are drawing a lot of attention due to their severe and irreversible consequences on human health. The animal industry is considered responsible in part because of the enormous volume of antibiotics used annually. In the current research, veterinary antibiotic (VA) degradation, finding the threshold of removal and recognizing the joint effects of chlortetracycline (CTC) and Tylosin combination on the digestion process were studied. Laboratory scale anaerobic digesters were utilized to investigate potential mitigation of VA in swine manure. The digesters had a working volume of 1.38 L (in 1.89-L glass jar), with a hydraulic retention time (HRT) of 21 days and a loading rate of 1.0 g-VS L−1 d−1. Digesters were kept at 39 ± 2 °C in incubators and loaded every two days, produced biogas every 4 days and digester pH were measured weekly. The anaerobic digestion (AD) process was allowed 1.5 to 2 HRT to stabilize before adding the VAs. Tests were conducted to compare the effects of VAs onto manure nutrients, volatile solid removal, VA degradation, and biogas production. Concentrations of VA added to the manure samples were 263 to 298 mg/L of CTC, and 88 to 263 mg/L of Tylosin, respectively. Analysis of VA concentrations before and after the AD process was conducted to determine the VA degradation. Additional tests were also conducted to confirm the degradation of both VAs dissolved in water under room temperature and digester temperature. Some fluctuations of biogas production and operating variables were observed because of the VA addition. All CTC was found degraded even only after 6 days of storage in water solution; thus, there was no baseline to estimate the effects of AD. As for Tylosin, 100% degradation was observed due to the AD (removal was 100%, compared with 24–40% degradation observed in the 12-day water solution storage). Besides, complete Tylosin degradation was also observed in the digestate samples treated with a mixture of the two VAs. Lastly, amplicon sequencing was performed on each group by using the 50 most variable operational taxonomic units (OTUs)s and perfect discriminations were detected between groups. The effect of administration period and dosage of VAs on Phyla Firmicutes Proteobacteria, Synergistetes and Phylum Bacteroides was investigated. These biomarkers’ abundance can be employed to predict the sample’s treatment group.