As a widespread emerging contaminant, chloramphenicol (CAP) adversely impacts ecological communities in the water environment. Biological treatment is widely used for aquatic pollutant removal, and the performance of functional microbes determines its outcome. Herein, a consortium with a powerful CAP-degrading capacity was domesticated from activated sludge. As the common degradation products of CAP, 4-nitrobenzoic acid (PNB) and 2,2-dichloroacetic acid (DCA) were also used as the sole substrates for long-term domestication. The successional pattern of the microbial community and critical functional genes through the 2.5-year domestication was revealed by metagenomic analysis. Sphingomonas, Caballeronia, and Cupriavidus became the most dominant populations in the CAP-, PNB-, and DCA-degrading consortia, respectively, and they were crucial degraders of PNB and DCA. Their collaboration contributed to the high mineralization rate of CAP. PNB was transformed into protocatechuic acid (PCA) and then mineralized through meta-cleavage and ortho-cleavage pathways. Crucial functional genes involved in CAP, PNB, and DCA metabolism, including CAP acetyltransferase, CAP oxidoreductase, haloacid dehalogenases, and protocatechuate dioxygenases, were significantly enriched in consortia. pH and carbon source had significant impacts on CAP biodegradation efficiency. The domesticated consortia and isolated strains are necessary microbial resources to enhance the bioremediation of CAP-, PNB-, or DCA-polluted environments.

• Three domesticated consortia could degrade CAP, PNB, and DCA with high efficiencies.

• A successional pattern of the microbial community across domestication was revealed.

• Collaboration of Sph., Cab., and Cup. contributed to a high CAP mineralization rate.

• Dynamic changes in key genes involved in CAP, PNB and DCA metabolism were deciphered.

• Carbon source and pH had significant impacts on the biodegradation efficiency of CAP.