The stability of two sequential moving bed bioreactor systems operated in anaerobic-anoxic-aerobic continuous moving bed bioreactor (CMBR: R1-R2-R3) and semi-continuous fed batch moving bed bioreactor (FMBR: B1-B2-B3) modes was assessed for phenol shock load (PSL) applications in the presence of thiocyanate and ammonia. Both the systems were exposed to 3000 mg phenol/L (PSL-I) and 3500 mg phenol/L (PSL-II) for 3 days each from initial 2500 mg phenol/L without any intermediate concentration at 6 days HRT (hydraulic retention time). The effect of PSL-I on R1 was reversible within 10-12 days. At PSL-II, R1 required 2 days stop of feed for stability and resumed removal efficiency of phenol (15%) and COD (3%). R2 remained robust to sustain both PSLs and recovered within 15 days from peak influent concentrations of 1727 mg phenol/L (removal: 67%) and 324 mg SCN--/L (removal: 68-70%). In B1, effluent COD increased by 2%, though effluent phenol decreased by 3% than the pre-shock condition after PSL-I exposure. B2 acted similar to R2 when exposed to PSLs. The effect of PSL-I on R3 and B3 was negligible. However, at PSL-II R3 became vulnerable for nitrification, whereas phenol, COD and SCN- removal remained unaffected. In B3, PSL-II caused a decrease in phenol, SCN- and NH+4-N removal. In B3, stop of feed for 4 days also did not improve nitrification. The performance of the CMBR system was better than that of the FMBR system for organic shock load exposure in the presence of multiple pollutants.