Pharmaceuticals enter ecosystems, which causes changes to microbial community structure and development of resistant genes. Anaerobic treatments can be an alternative application for treatment of pharmaceutical wastewaters, which has high organic content. This study aims to develop an understanding of the effects of sulfamethoxazole–erythromycin–tetracycline (ETS), sulfamethoxazole–tetracycline (ST), erythromycin–sulfamethoxazole (ES) and erythromycin–tetracycline (ET) combinations on the anaerobic treatment of pharmaceutical industry wastewater. The results of this investigation revealed that bacteria have a competitive advantage over archaea under all antibiotic combinations. The ET reactor showed a better performance compared to other reactors; this could be due to antagonistic effects of sulfamethoxazole. Acute inhibition in the microbial community was also strongly affected by antibiotics concentrations. This indicated that the composition of the microbial community changed in association with anaerobic sequencing batch reactor performances. The results of this research support the idea that an acute test could be used to control and improve the anaerobic treatment system.