Iron is one of the most frequently utilized transition metal in the biosphere and plays a crucial role in the biogeochemical cycles of soil elements. The direct interplay between aqueous Fe(II) (Fe(II)_aq) and the structural Fe(III) in iron (hydr)oxide is the recently found important process of soil iron cycle. Previous studies focused on the chemical mechanism of Fe(II)_aq-induced recrystallization and phase transformation of iron (hydr)oxide. However, microorganism often coexists with iron (hydr)oxide in the soil environment, and plays an important role in the iron cycle process. The effect of microorganisms, especially iron-reducing bacteria, on the interplay between Fe(II)_aq and the structural Fe(III), and the phase transformation of iron (hydr)oxide remain unclear. In this study, we focus on the effect of iron-reducing bacteria, Shewanella oneidensis MR-1 (hereafter MR-1), and herein the influencing mechanisms on the phase transformation of lepidocrocite induced by Fe(II)_aq. Enriched ⁵⁷Fe isotope tracer studies demonstrate that Fe(II)_aq undergoes electron transfer and atom exchange with lepidocrocite, and results in 63.5% of structural Fe(III) atoms in lepidocrocite exchanging with 1.0 mM Fe(II)_aq in solution at pH 7.0 for 23 days. XRD analysis results show that part of lepidocrocite is transformed into goethite after 23 days incubation. Interestingly, amended with Fe(II)_aq and active cells (MR-1), lepidocrocite can be reduced and the concentration of Fe(II) in solution increases quickly, which further enhance the rate of Fe atom exchange. Lepidocrocite is transformed into magnetite during this process. However, Mössbauer analysis results show that lepidocrocite could be recrystallized as lepidocrocite and goethite after incubation 23 days in the abiotic experiment of Fe(II)_aq and lepidocrocite, and lepidocrocite, goethite and magnetite were found in the presence of MR-1. Hence, we could infer that the presence of iron-reducing bacteria could change the Fe(II)_aq concentration which would further change the iron atom exchange and phase transformation of lepidocrocite. The initial Fe(II)_aq could exchange with lepidocrocite directly, and lepidocrocite was recrystallized as lepidocrocite and goethite; or coupled with Fe(II)_aq produced by iron-reducing bacteria, exchanged with structural Fe(III), and lepidocrocite was recrystallized as magnetite.