Releasing of dye-containing wastewater by the textile industry into general water bodies can adversely affect aquatic ecosystems and human health. The objective of this study is to assess the Congo red dye biodegradation and detoxification by immobilized Aspergillus niger obtained from textile dye wastewater. The effects of process parameters like pH, temperature, reaction time and initial concentration on Congo red degradation were studied. Equilibrium adsorption isotherms, kinetics and thermodynamics were also investigated. The experimental data were analyzed by the Langmuir, Freundlich and Temkin models of adsorption. The adsorption isotherm data fitted well to Langmuir isotherm and the kinetic data fitted well to the pseudo-second-order model. The degraded metabolites of Congo red were characterized by using UV–Vis spectrophotometer, Fourier transform infrared spectroscopy and high-performance liquid chromatography, further confirmed that biodegradation of Congo red was due to reduction of the azo bond. Phytotoxicity test confirmed that degradation metabolites were a less toxic than original dye. The reusability of the immobilized Aspergillus niger was repeated with six cycles and removal efficiency ranged from 98 to 72%. The results in this study substantiate that immobilized Aspergillus niger could be employed as a good adsorbent for the removal of Congo red dye from wastewater.