Effluents from the textile industry are an active problem in the sector and one of the world’s main environmental problems. The conventional treatments applied are not always efficient in terms of compliance with legislation, and, in many cases, the efficiency of treatment is guaranteed by the enormous energy expenditure involved, camouflaging the momentary problem and not effectively treating it. In this work, batch reactors with immobilized biomass of Aspergillus niger AN400 were arranged in series for the treatment of real textile wastewater containing approximately 20 mg/L of indigo carmine. Sucrose was added as a co-substrate in concentrations of 1 g/L and 0.5 g/L, in the first and second reactors, respectively, over 19 cycles of 48 h. The highest decolorization rate in the system was (93 ± 4) %, with the largest amount removed in the first reactor (90 ± 6) %, occurring mainly by biological means. The production of aromatic by-products from the initial degradation of the dye molecule was reflected in the lower removal efficiency of dissolved organic matter: 52% in the first reactor, and 25% in the second reactor. The number of colonies of fungi was higher than that of bacteria, 2.24:1 and 2.44:1 in the first and second reactors, respectively. The treated effluent in the system showed less toxicity than the raw effluent, and this demonstrates the potential of this technology in the treatment of textile effluents containing indigo carmine.