Zero-valent iron (ZVI) has been widely applied to the remediation of uranium (U)-contaminated water. Notably, indigenous bacteria may possess potential positive or unfavorable influence on the mechanism and stability of Fe-U precipitates. However, the focus of the researches in this field has mainly been on physical and/or chemical aspects. In this study, batch experiments were conducted to explore the effects of an indigenous bacterium (Leifsonia sp.) on Fe-U precipitates and the corresponding removal efficiency by ZVI under different environmental factors. The results showed that the removal rate and capacity of U(VI) was significantly inhibited and decreased by ZVI when the pH increased to near-neutral level (pH = 6~8). However, in the ZVI + Leifsonia sp. coexistence system, the U(VI) removal efficiency were maintained at high levels (over 90%) within the experimental scope (pH = 3~8). This revealed that Leifsonia sp. had a synergistic effect on U(VI) remove by ZVI. According to scanning electron microscope and energy dispersive X-ray detector (SEM-EDX) analysis, dense scaly uranium-phosphate precipitation was observed on ZVI + Leifsonia sp. surface. The X-photoelectron spectroscopy (XPS) and Fourier transform infrared spectroscopy (FTIR) analysis indicated that Leifsonia sp. facilitated the generation of U(VI)-phosphates precipitates. The X-ray diffraction (XRD) analyses further revealed that new substances, such as (Fe(II)Fe(III)2(PO4)2(OH)2), Fe(II)(UO2)2(PO4)2·8H2O, Fe(II)Fe(III)5(PO4)4(OH)2·4H2O, etc., were produced in the coexisting system of ZVI and Leifsonia sp. This study provides new insights on the feasibility and validity of site application of ZVI to U(VI)-contaminated subsurface water in situ. Graphical abstract.