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Biocompatible materials and biocarriers have attracted great attention in biological wastewater treatment owing to their excellent performance in improving pollutant removal. Graphene-based material, a biocarrier candidate, with excellent adsorbability and conductivity was increasingly applied in anaerobic digestion due to its exceptional potential in the adsorption and electron transfer process. Nevertheless, the green approach for the formation of bio-graphene complexes and their mechanism in dye removal is limited. The aim of this study is to investigate and assess the performance of biological graphene hydrogel (BGH) formed by Shewanella putrefaciens CN32 on the removal of methyl orange (MO) and methylene blue (MB). The results showed that the formation of BGH is determined by the physicochemical characteristics of graphene oxide, including sheet size, oxidation degree, and interlayer distance. BGHs significantly increased the removal efficiency of dyes in comparison to non-graphene samples, with a 24-h removal rate of MO and MB reaching 92.9% and 91%, respectively. The synergetic mechanism of BGH on the enhanced removal rate of organic dye can be ascribed to GO's ability in accelerating extracellular electron transfer and stimulating biodegradation pathways relating to c -type cytochromes, including MtrA and MtrC. These findings provided an understanding of the relationship between graphene-based nanomaterials and Shewanella , which facilitated their future application in environmental biotechnology. [Display omitted] • The reduction of GO by S. putrefaciens CN32 prompt BGH generation. • Sheet area and degree of defects of GO determine the BGH formation. • Bacteria-immobilized rGO hydrogel displayed a synergistic effect in bioremediation. • BGH increased dye removal efficiency by accelerating extracellular electron transfer. [ABSTRACT FROM AUTHOR]