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Submerged macrophyte restoration and in situ phosphorus (P) passivation are effective methods for the control of internal P loading from sediments. This study explored the synergistic effects of <i>Vallisneria natans</i> and iron (Fe)-oxidizing bacteria (IOB) on internal P loading from eutrophic freshwater lake sediments by taking into account Fe-bound P (FeP) formation and associated bacterial community structures. Sediment samples were prepared in glass tanks under four treatments, namely no <i>V. natans</i> planting or IOB inoculation (control), planting <i>V. natans</i> without IOB inoculation (Va), planting <i>V. natans</i> with IOB inoculation (Va-IOB), and planting <i>V. natans</i> with autoclaved IOB inoculation (Va-IOB[A]). Compared with the control, all three treatments with <i>V. natans</i> (Va, Va-IOB, and Va-IOB[A]) had significantly decreased organic matter contents and increased redox potential in sediments (<i>p</i> < 0.05), at the rapid growth and mature stages of <i>V. natans</i>. Planting <i>V. natans</i> with and without IOB inoculation also decreased the total P (TP) and Fe–P concentrations in sediments. Conversely, Fe³⁺ concentrations, Fe³⁺/Fe²⁺ ratios, and the proportions of Fe–P in TP all increased in sediments planted with <i>V. natans</i>, especially under the Va-IOB treatment (<i>p</i> < 0.05). Furthermore, bacterial community diversity increased in sediments due to the presence of <i>V. natans</i>. The relative abundances of IOB (including <i>Acidovorax</i> and <i>Chlorobium</i>) increased from the transplanting to the rapid growth stage of <i>V. natans</i> and then decreased afterwards. In the later stages, the relative abundances of IOB and their ratios to Fe-reducing bacteria were the highest under the Va-IOB treatment. Accordingly, synergistic interactions between <i>V. natans</i> and IOB could enhance Fe–P formation and reduce TP concentrations in eutrophic lake sediments by altering sediment physicochemical properties and Fe oxidation-related bacterial community structures.