The presence of unused dyes and dye degradation intermediates in the textile industry wastewaters is the major challenge in its treatment. A wide range of treatments including various physicochemical processes are used for this wastewater. Incomplete dye degradation results in hazardous colorless aromatic amine intermediates that are teratogenic in nature. A synergistic plant-microbe system operated in a sequential anaerobic-aerobic mode was evaluated for the complete degradation of a model azo dye methyl red under laboratory conditions. The degradation of methyl red and its break down products 2-aminobenzoic acid and N,N-dimethyl-p-phenylenediamine were analysed by HPLC, FTIR and GC-MS. The vetiver-microbe system had shown enhanced dye degradation. The dye decolourization percentage achieved for integrated plant-microbe treatment system (T) after anaerobic condition was 53.5 ± 6.2% and aerobic condition was 92 ± 3.4%. The removal efficiency of the intermediates 2-ABA and DMPD was found to be 89.79% in the integrated plant-microbe treatment system. The plant-microbe system was most effective in the removal of toxic aromatic amine as seen by lesser phytotoxicity for seed germination and teratogenicity in case of zebrafish development in the treated water.