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Abstract The comparison of long-term ceramic membrane bioreactors (MBRs) without and with in-situ ozonation was investigated in this study in terms of membrane fouling, activated sludge, effluent quality and microbial community in wastewater treatment. The optimal dosage of in-situ ozonation for long-term MBR operation was firstly determined as 5 mg/L (0.66 mg-ozone/g-mixed liquor suspended solid (MLSS)) with the optimal filterability of mixed liquor. During the long-term filtration experiment, MBR-ozone with in-situ ozonation demonstrated its significantly alleviated ceramic membrane fouling performance compared with MBR-control without in-situ ozonation as a result of the enhanced filterability of mixed liquor and organic foulants removal from membrane surface by in-situ ozonation oxidation. Furthermore, ozonation was beneficial to phosphorus removal and the total phosphorus (TP) concentration in effluent of MBR-control (0.82 ± 0.63 mg/L) was >2-fold higher than that of MBR-ozone (0.29 ± 0.41 mg/L). The improved phosphorus removal performance by ozonation was due to the increased abundance of phosphate accumulating bacteria of Candidatus Accumulibacter in activated sludge. However, ozonation was detrimental to nitrogen removal mainly as a result of the inhibition of denitrification with the decreased relative abundance of denitrification genus of Dechloromonas in activated sludge. Overall, ceramic MBR with in-situ ozonation had not only significantly alleviated membrane fouling but also remarkably improved phosphorus removal performance. Graphical abstract Unlabelled Image Highlights • Long-term ceramic MBRs without and with in-situ ozonation were compared. • The optimal filterability of mixed liquor was achieved at ozone dosage of 5 mg/L. • In-situ ozonation significantly alleviated ceramic membrane fouling. • Ozonation was beneficial to phosphorus removal but detrimental to nitrogen removal. • Microbial community of activated sludge was significantly changed by ozonation. [ABSTRACT FROM AUTHOR]