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A novel hybrid fed-batch moving-bed bioreactor (MBBR) system was developed for the treatment of refinery wastewater containing a wide range of phenol (250–1,000 mg/L) and ammonia-nitrogen (50 mg/L) using an indigenous mixed microbial culture. A hybrid system containing a native mixed microbial consortium and comprising three MBBR units connected in series and operating with a 24-day hydraulic retention time (HRT) and a recycle ratio of 1.0 was evaluated under three environmental conditions. MBBR units in the system were operated in anaerobic, anoxic, and aerobic conditions in fed-batch mode. The hybrid system proficiently removed the phenol (99%), ammonia-nitrogen (95%), and reduced chemical oxygen demand (COD) (98%) from maximum feed concentrations of 1,000, 50, and 3,077±6 mg/L , respectively. The overall NH4-N removal efficiency of the system decreased by 4.7%, and COD reduction efficiency increased by 2% while varying the feed phenol concentration from 250 to 1,000 mg/L. However, the removal rate for phenol (20.72 to 82.42 mg/L·day) and NO3-N (10.57 to 17.81 mg/L·day) increased in the anaerobic and anoxic reactor, respectively. The ammonia removal rate for the aerobic reactor decreased from 8.14 to 7.377 mg/L·day. Ultraviolet (UV)-visible spectroscopy and gas chromatography-mass spectroscopy (GC-MS) were used to identify the formation of intermediates (catechol and muconic acid) during the biotransformation of phenol. Scanning electron microscopy (SEM) analysis showed better adhesion of the mixed microbial community in the pores of the carrier media. The best fit of the modified Stover-Kincannon model confirmed that phenol and NH4-N utilization is a function of organic loading rate under steady-state conditions. The results of this investigation suggest that the newly developed hybrid system with indigenous mixed microbes can treat the heterogeneous pollutants discharged in refinery wastewater. [ABSTRACT FROM AUTHOR]