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The magnetic signals of magnetite nanoparticles (NPs) preserved in rocks, soils, and sediments are effective index for paleoenvironmental reconstruction. It has been demonstrated that magnetite NPs can serve as a terminal electron sink for the microbial respiration (i.e., microbial iron reduction). The magnetic properties of magnetite NPs may be altered by microbial iron reduction, which is a critical but often overlooked process in paleomagnetism. In this study, three magnetite NPs with different particle sizes were reduced by a dissimilatory iron‐reducing bacterium (Shewanella oneidensis MR‐1) under a non‐growth condition mimicking that of the early Earth and modern oligotrophic environment. The changes in magnetic, chemical as well as crystallographic properties of the magnetite NPs during the microbial reduction process were examined. Our results showed that the bioreduction rate of magnetite NPs was …