Coke-oven wastewater discharged from the steel-manufacturing process is phenol and thiocyanate (SCN)-rich wastewater, which inhibits microbial activities in biological wastewater treatment processes. In the present study, synergistic inhibition of anaerobic ammonium oxidation (anammox) activity by phenol and SCN was examined by batch incubation and continuous operation of an anammox reactor. The comparison of anammox activities determined in the batch incubation, in which the anammox biomass was anoxically incubated with 10–250 mg L−1 of i) phenol, ii) SCN, or iii) both phenol and SCN, showed that synergistic inhibition by phenol and SCN was greater than the inhibitions by phenol or SCN alone. The synergistic inhibition by phenol and SCN was further investigated by operating an up-flow column anammox reactor for 262 d. The removal efficiencies of NH4+ and NO2− deteriorated when phenol and SCN concentrations in the influent increased to 16 and 32 mg L−1, respectively, and the inhibition of anammox activity was further investigated by a15NO2− tracer experiment. Addition of phenol and SCN resulted in a population shift of anammox bacteria, and the dominant species changed from “Candidatus Kuenenia stuttgartiensis” to “Ca. Brocadia sinica”. The relative abundance of Azoarcus and Thiobacillus 16S rRNA gene reads increased during the operation, suggesting that they were responsible for the anaerobic phenol and SCN degradation. The present study is the first to document the synergistic inhibition of anammox activity by phenol and SCN and the microbial consortia involved in the nitrogen removal as well as the phenol and SCN degradations. Display omitted •For the first time, anammox reactor fed with phenol and SCN was operated.•Phenol and SCN at 100 mg L−1 decreased >90% of anammox activity for short term.•Phenol and SCN at 16–32 mg L−1 deteriorated N-removal performance for long term.•Shift in anammox population from Ca. Kuenenia to Ca. Brocadia were observed.•Azoarcus and Thiobacillus bacteria are the potential phenol and SCN degraders.