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In this study, a hydrogen-based denitrification (HD) reactor was used to investigate the simultaneous treatment of nitrogen and decolorization in textile wastewater contaminated with organic matter. The reactor operated in two phases: without and with organic matter. Despite the short hydraulic retention time, the HD system successfully removed all pollutants, including nitrate, nitrite, reactive black-5 dye and chemical oxygen demand. The unhindered treatment efficiency for nitrogen and decolorization in the presence of organic pollutants was observed. With the addition of organic matter, the nitrogen removal efficiency increased slightly from 85% to 90–100%, and the decolorization rate doubled from 25% to 50–60%. Organic matter played a crucial role in stimulating heterotrophic bacteria during biological denitrification and acted as a carbon source facilitating biological denitrification and azo bond cleavage during dye degradation. Despite the generation of toxic byproducts and changes in the dominant microbial community, the treatment efficiency remained stable and improved. This approach offers a promising solution for enhancing treatment efficiency in textile wastewater, providing a cost-effective and environmentally friendly option for developing countries to treat wastewater before discharge.