Biogenous iron oxide (L-BIOX) produced by Leptothrix ochracea aquatic bacteria, which is an amorphous Fe3+-based oxide that contains Si4+ and P5+ with tube-formed structures, has been studied for practical use as a conversion anode for lithium secondary batteries. L-BIOX has a capacity approximately two times larger than that of graphite. Conductive additives such as carbon nanotubes (CNTs) and Ketjen black (KB), of which the size and surface area are comparable to the primary nanoparticles of L-BIOX, are required to achieve good electrical contacts. Quasi-open circuit voltage (OCV) and X-ray photoelectron spectroscopy (XPS) measurements with respect to the discharge reveal that the conversion reaction occurs and solid electrolyte interphase (SEI) films are formed within the potential plateau area (1.8–1.5 V vs. Li). The water contained in L-BIOX is completely removed by heat-treatment at 400 °C. The elimination of water decreases the first irreversible capacity and improves the cycle performance. Li pre-doping by contact with Li metal realizes 100% coulombic efficiency at the first cycle. A lithium ion cell fabricated with a Li-pre-doped L-BIOX anode and a LiCoO2 cathode exhibits good cycle performance with high capacity retention.