The occurrence and removal of estrone (E1), 17β-estradiol (E2), and 17α-ethinylestradiol (EE2) as typical steroid estrogens (SEs) and the bacterial community structure in a full-scale anaerobic/anoxic/aerobic-membrane bioreactor (A2O-MBR) process were investigated. Residual E1 and EE2 were detected in the effluent, while the excess sludge remained all types of SEs. The biodegradation of SEs occurred primarily in the aerobic tank and the sorption capacity of SEs on activated sludge decreased along the flow course. The internal recirculation ratio applied in the A2O-MBR process failed to form distinct redox conditions. Water temperature was the predominant factor affecting bacterial community composition and SEs biodegradation. Genera not previously reported as SE biodegraders might be responsible for SEs biodegradation in full-scale processes exposed to environmentally relevant SEs concentrations. Heterotrophic cometabolism was inferred as the primary SEs biodegradation mechanism. The present study revealed the correlations between operational factors and SEs biodegradation and the significance of enriching bacterial populations responsible for SEs biodegradation to improve the potential of A2O-MBR process as a SEs barrier.