This study aims to develop a predictive framework to assess the removal and fate of trace organic chemicals (TrOCs) during wastewater treatment by anaerobic membrane bioreactor (AnMBR). The fate of 27 TrOCs in both the liquid and sludge phases during AnMBR treatment was systematically investigated. The results demonstrate a relationship between hydrophobicity and specific molecular features of TrOCs and their removal efficiency. These molecular features include the presence of electron withdrawing groups (EWGs) or donating groups (EDGs), especially those containing nitrogen and sulphur. All seven hydrophobic contaminants were well removed (>70%) by AnMBR treatment. Most hydrophilic TrOCs containing EDGs were also well removed (>70%). In contrast, hydrophilic TrOCs containing EWGs were mostly poorly removed and could accumulate in the sludge phase. The removal of several nitrogen/sulphur bearing TrOCs (e.g., linuron and caffeine) by AnMBR was higher than that by aerobic treatment, possibly due to nitrogen or sulphur reducing bacteria.