Adsorption and bio-reduction are preferred methods for the Cr(VI) removal due to its toxicity and carcinogenicity. However, the migration and transformation mechanisms of Cr(VI) in the natural ferrihydrite (Fh)-humic acid (HA)-Cr(VI) (Fh-HA-Cr) coprecipitation ternary system in the presence of Shewanella putrefaciens remain unclear. Fh-HA-Cr coprecipitations were synthesized by regulating OC/Fe and cultured in the presence of S. putrefaciens while controlling pH and Fe(II). Results revealed that the fate and speciation of Cr(VI) involve the following pathways. Firstly, acidic conditions accelerate Cr(VI) adsorption by coprecipitation, which diminishes in the presence of S. putrefaciens. Meanwhile, exogenous HA promotes redox on the surface of Fh-HA-Cr co-precipitates under acidic conditions, facilitating Cr(VI) conversion into Cr(III). Secondly, HA and Fe(II) jointly mediate the Cr(VI) reduction in the presence of S. putrefaciens under neutral conditions. Thirdly, the adsorbed Cr(VI) and reduced Cr(III) are incorporated into coprecipitation in the presence of S. putrefaciens, inhibiting Cr desorption under neutral conditions. Our findings highlight the significant roles of S. putrefaciens in the adsorption and reduction of Cr(VI) during Fh-HA-Cr coprecipitation transformation, providing a theoretical basis for Cr(VI) removal.