Immobilization of uranium (VI) via uranium-phosphate (U-P) precipitation exhibits a great potential in remediation of uranium in contaminated environments. However, phosphorus as a vital element of bacteria, the decomposition, absorption and transformation of phosphorus may affect the stability of uranium with aging time. The main purpose of this work is to study the effect of bacteria on uranium sequestration mechanism and stability by different forms of phosphorus in a water sedimentary system. The results showed that addition of phosphate effectively enhanced uranium removal rate, with the highest removal rate of 99.84%. According to the X-Ray Diffraction (XRD), Scanning Electron Microscopy and Energy Dispersive Spectrometer (SEM-EDS) analyses, the fugitive positions of phosphorus and uranium elements remained essentially the same on the sediment surface, meanwhile the appearance of more pronounced phosphorus and uranium signal peaks confirmed the existence of U-P precipitates. X-ray Photoelectron Spectroscopy (XPS) analyses imply that hexavalent uranium and tetravalent uranium co-exist in the precipitate. Combined with BCR results, bacteria and phosphorushave a synergistic effect on uranium immobilization, although there will be a small part of uranium release due to the action of bacteria with the extension of time. Collectively, the results demonstrated that bacteria and phosphorus could effectively mediate U-P precipitates, realizing the transformation and immobilization of uranium from a transferable phase to a stable phase. The experimental findings could provide theoretical evidence for uranium immobilization in uranium-contaminated groundwater sediment.