The production of excess sludge by the activated sludge system of wastewater treatment plants is a problem. In this study, the EPS characteristics on production and degradation were investigated in the real-scale food processing wastewater treatment system (i.e., a micro-aerobic reactor coupled with a membrane bioreactor (MAR-MBR)) with a treatment capacity of 150 t d−1, which could cater for the low production of excess sludge (i.e., 9 t·a−1; 76% moisture content). The total organic carbon concentrations in the different EPS fractions were in the following order: soluble EPS (S-EPS) < loosely bound EPS (LB-EPS) < tightly bound EPS (TB-EPS). Although the components (e.g., protein and humic acid-like substances) of each EPS fraction changed significantly throughout the MAR-MBR process owing to the low production of excess sludge, the degrees of change in S-EPS, LB-EPS, and TB-EPS were significantly different from the corresponding change in their relative molecular weights. Furthermore, the microbial community composition was beneficial for the release and degradation of EPS, and the regulation of gene functions via the MAR-MBR enhanced this process. Display omitted •Excess sludge was minimized in micro aerobic reactor coupled with membrane bioreactor.•The order and degree of change in three fractions of EPS were significantly different.•Aerobic and facultative bacteria converted EPS.•Regulation of gene functions made EPS conversion easily during MAR-MBR process.