This study examined the microbial synthesis of magnetite and Pd/Zn-substituted magnetite using metal-reducing bacteria (Clostridium sp.), and the mineralogical characteristics of various types of magnetite formed initially and transformed minerals aged for 5 years. XRD, SXRD, and TEM-EDS analyses were used to characterize the mineralogy, crystal structure, chemistry, shape, and size distribution of the magnetites and transformed minerals. The metal-reducing bacteria reduced akaganeite and Pd/Zn-akaganeite to magnetite and Pd/Zn-substituted magnetite using glucose as an electron donor, respectively. Metal substitution of Pd and Zn within the magnetite structure resulted in a decrease in the unit-cell parameter of the magnetite crystals. After 5 years, the biogenic magnetite showed changes in unit-cell parameters and transformation to siderite during prolonged cultivation under anaerobic conditions. These results indicate that long-term aging may affect the mineralogical transformation and alter the nano-sized crystal structure.