Microbial Cr(Ⅵ) reduction represents a cost-effective remediation approach, yet its application in continuous-flow systems is often constrained by toxicity inhibition and nutrient instability. This study developed an integrated microbial—phosphorus mineral—corncob (MPC) composite, which encapsulates Cr(Ⅵ)-reducing bacteria with slow-release nutrients within a hydrogel matrix. The MPC system sustained complete Cr(Ⅵ) removal at influent concentrations up to 160 mg/L in synthetic wastewater and 120 mg/L in actual groundwater, conditions under which conventional systems typically fail. Reactive transport modeling revealed that diffusion limitations create protective intraparticle concentration gradients, while density functional theory (DFT) calculations confirmed strong Cr(Ⅲ) sequestration and sustained phosphorus bioavailability. The estimated treatment cost is competitive with existing technologies. These findings demonstrate that engineering a protected self-sufficient microbial microenvironment can overcome critical stability limitations in Cr(Ⅵ) bioremediation.