This study evaluates the process performance of a real-scale anaerobic baffled reactor (ABR) coupled with swim bed tank (SBT) as an aerobic post-treatment process in treating fishmeal wastewater discharged from an actual fishmeal processing factory in Bali, Indonesia. The industrial wastewater released from the aforementioned factory contains high concentrations of organic COD (more than 10 g COD·L−1) and ammonia (100 to 200 mg-N·L−1). During the study period, ABR demonstrated a high organic removal of 95.7 ± 2.9%, with an organic loading rate of 2.1 ± 1.3 kg COD·m−3·day−1. Furthermore, the average total COD influent and effluent of the proposed system were 37,800 ± 15,000 mg COD·L−1 and 435 ± 113 mg COD·L−1, respectively, during the entire experimental period. Based on the determination of volatile fatty acids (VFAs) and microbial community analysis of the ABR-retained sludge, the first and second columns of the ABR were utilized as hydrolysis zones and the third column functioned as an acidification zone. The remaining columns were used for methane production and as final removal zones. The results concluded that this system has the potential to treat fishmeal wastewater under onsite industrial conditions.