This study explores the effectiveness of an integrated anaerobic membrane bioreactor (AnMBR) coupled with an anoxic/oxic membrane bioreactor (A/O MBR) for the treatment of natural rubber industry wastewater with high sulfate, ammonia, and complex organic contents. This study was conducted at the lab-scale over a duration of 225 days to thoroughly investigate the efficiency and sustainability of the proposed treatment method. With a hydraulic retention time of 6 days for the total system, COD reductions were over 98%, which reduced the influent from 22,158 ± 2859 mg/L to 118 ± 74 mg/L of the effluent. The system demonstrates average NH3-N, TN, and total phosphorus (TP) removal efficiencies of 72.9 ± 5.7, 72.8 ± 5.6, and 71.3 ± 9.9, respectively. Despite an average whole biological system removal of 50.6%, the anaerobic reactor eliminated 44.9% of the raw WW sulfate. Analyses of membrane fouling revealed that organic fouling was more pronounced in the anaerobic membrane, whereas aerobic membrane fouling displayed varied profiles due to differential microbial and oxidative activities. Key bacterial genera, such as Desulfobacterota in the anaerobic stage and nitrifiers in the aerobic stage, are identified as instrumental in the biological processes. The microbial profile reveals a shift from methanogenesis to sulfide-driven autotrophic denitrification and sulfammox, with evidence of an active denitrification pathway in anaerobic/anoxic conditions. The system showcases its potential for industrial application, underpinning environmental sustainability through improved wastewater management.