Anaerobic membrane bioreactors (AnMBRs) offer a promising solution for wastewater treatment, combining anaerobic digestion with membrane filtration to efficiently remove pollutants and mitigate the spread of antibiotic resistance genes (ARGs). The impact of antibiotic mixtures on AnMBR performance and ARG profiles remains crucial to investigate due to their prevalence in various environments. This study examined the effects of an amoxicillin and flucloxacillin mixture on key operational parameters in an AnMBR system. The AnMBR demonstrated resilience to the antibiotic mixture, maintaining a high average chemical oxygen demand (COD) removal efficiency (91 ± 4.5%) and stable biogas production (713 ± 150 L/d) even at elevated antibiotic concentrations (250 μg/L). However, antibiotic presence significantly influenced ARG profiles within the biomass and effluent, highlighting the complex interplay between antibiotic exposure and resistance gene dynamics. These findings emphasize the importance of understanding and optimizing AnMBR performance under antibiotic pressure to mitigate the spread of antibiotic resistance while ensuring effective wastewater treatment and resource recovery.