Natural iron-oxides are often found in close association with bacterial cells in aquatic environments, but the effect of bacteria on their formation is still under investigation. The present study was undertaken to assess the effect of two common bacteria, Bacillus subtilis and Escherichia coli, on the morphology and mineralogy of Fe oxides. All Fe oxides were synthesised by oxidation of Fe(II) (2 × 10−4 M) at pH = 7. Three systems were studied, i.e., abiotic Fe oxides, Fe oxides formed in the presence of bacteria (which we call “biogenic” Fe oxides) and abiotic Fe oxides mixed with bacterial cells. Samples were analysed by X-ray diffraction (XRD) and transmission electron microscopy (TEM). Fe oxide particles in all systems showed a needle-like morphology, with many needles seeming to be attached to a sheet, and were identified as lepidocrocite. However, the biogenic lepidocrocite crystals were generally shorter than the abiotic ones, and the crystals were found in association with the bacterial cell-wall, especially with B. subtilis, a Gram-positive bacterium. Biogenic lepidocrocite crystals also displayed an attenuation of the XRD 120 line, which is indicative of a low crystallinity. Growth limitation and poor crystalline order are then likely to affect the surface area of Fe oxides and indirectly, their sorptive capacity.