Zero-valent iron (Fe0) has been extensively used in hexavalent chromium (Cr(VI)) removal from groundwater, but its treatment suffers from interference of humic acid (HA) and ferrochrome precipitate. In this study, a biotic Fe0 system was established to address these problems in Cr(VI) removal from HA-rich groundwater by introducing a combination of heterotrophic and hydrogen-autotrophic microorganisms. Due to the formation of HA-Fe complexes and ferrochrome precipitates on the Fe0 surface, the HA-abiotic Fe0 system obtained a slight Cr(VI) removal of 10.5%. While in the HA-biotic Fe0 system, heterotrophic microbes could effectively eliminate HA through biodegradation and decrease HA-Fe complex generation; autotrophic microbes used H2 from iron corrosion as electron donors for their metabolism and promoted iron corrosion and active secondary mineral generation (e.g., magnetite and green rust) for Cr(VI) adsorption and reduction. Therefore, a much higher Cr(VI) removal of 84.9% was achieved. Additionally, increasing HA content and extra electron acceptors (e.g., sulfate and nitrate) both boosted Cr(VI) removal, further proving the role of heterotrophic microbes in biodegrading HA for enhanced Cr(VI) elimination. This work presented a feasible strategy to achieve efficient Cr(VI) removal with Fe0 by diminishing HA interference and ferrochrome precipitate passivation through the synergistic effect of heterotrophic and hydrogen-autotrophic microorganisms.