In the present study, Chryseobacterium geocarposphaerae DD3 isolated from textile industry dye effluent in West Bengal, India, displayed significant tolerance to sulfonated di-azo dye Congo red (CR), up to 500 ppm. The optimum decolourisation revealed that C. geocarposphaerae DD3 was capable of 96.52% decolourisation of 0.2 g L−1 CR within 12 h of treatment in the presence of 5 g L−1 glucose as supplementary carbon source. Biodegradation analysis of decolourised CR containing water was investigated by FTIR, MS and 1H NMR, which confirmed the absence of azo bond as well as the toxic aromatic amines. Further, phytotoxicity analysis was performed to assess the toxicity of CR before and after bacterial treatment. Growth indexes of Vigna radiata L. seed confirmed that the biodegraded water was non-phytotoxic in comparison to the control CR solution. Multivariate analyses confirmed the same, showing significant differences between measured plant health indicators for CR solutions, whereas no significant differences were found between distilled and treated water. This study is novel as it is the first report of dye degradation by C. geocarposphaerae and may lead to a sustainable way of treating dye-contaminated water in the near future.