Discharges of disposal of the textile industry into general water bodies can cause deterioration of aquatic ecosystems and adversely affect human health. The objective of this study is to assess the Congo red dye decolourization by immobilized Aspergillus niger obtained from textile dye wastewater. The effect of experimental parameters like pH 5, contact time (30 h) and initial dye concentration (50 mg/L) on the process of decolourization of dye in the aqueous solution was revealed 97%. The optimum dye decolourization efficiency of immobilized Aspergillus niger using central composite design was found to be 98.97%, obtained were pH 5, initial concentration 50 mg/L, temperature 30 °C and contact time 36 h. Isotherm studies showed that the experimental data better fitted with to Langmuir isotherm, the Freundlich isotherm and Tempkin isotherm for decolourization dye by immobilized Aspergillus niger. It was found that the decolourization was best evaluated by a pseudo-second-order model rather than the pseudo-first-order model. The maximum monolayer adsorption capacity of immobilized Aspergillus niger was resulted as 4325 mg/g at 303 K (R² = 0.994). The value of separation factor (RL) from Langmuir equation and Freundlich constant (n) indicated on favorability of bioabsorption. Thermodynamic parameters such as ΔG°, ΔH° and ΔS° were calculated and the negative value of ΔH° (− 29,671 kJ/mol) for corresponding initial Congo red dye concentrations: 50 mg/L, in the solution indicated that the bioabsorption was of exothermic reaction.. The UV–Vis and FTIR analysis of metabolites after treatment confirmed that the decolourization. Phytotoxicity test confirmed that was less toxic than original dye. The reusability of the immobilized Aspergillus niger was repeated with seven cycles and removal efficiency ranged from 98 to 42%.