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This study explored the effect of eight antimicrobials on the efficiency of biogas production in the anaerobic digestion (AD) process of cattle manure. The microbiome involved in AD, presence and number of genes <i>mcr</i>A, <i>MSC</i> and <i>MST</i> specific for <i>Archaea</i>, and antibiotic resistance genes (ARGs) concentration in digestate (_D) were examined. Supplementation of antibiotics to substrate significantly lowered biogas production. Amoxicillin caused a 75% decrease in CH₄ production in comparison with the control samples. Enrofloxacin, tetracycline, oxytetracycline, and chlortetracycline reduced the amount of biogas produced by 36, 39, 45 and 53%, respectively. High-throughput sequencing of 16S <i>r</i>RNA results revealed that bacteria dominated the <i>Archaea</i> microorganisms in all samples. Moreover, antibiotics led to a decrease in the abundance of the genes <i>mcr</i>A, <i>MSC</i>, <i>MST</i>, and induced an increase in the number of tetracyclines resistance genes. Antibiotics decreased the efficiency of the AD process and lowered the quantity of CH₄ obtained, while stimulating an increase in the number of ARGs in _D. This work reveals how antimicrobials affect the cattle manure AD process and changes in microbial biodiversity, number of functional genes and ARGs in the digestate due to drugs exposure. It also, provides useful, practical information about the AD process.