Subsurface redox fronts control the mobilization and fixation of many trace elements, including potential pollutants such as certain radionuclides. Any safety assessment for a deep geological repository for radioactive wastes needs to take into account adequately the long-term redox processes in the geosphere surrounding the repository. To build confidence in understanding these processes, a redox front in a reduced siliceous sedimentary rock distributed in an uplifting area in Japan has been studied in detail. Geochemical analyses show increased concentrations of Fe and trace elements, including rare earth elements (REEs), at the redox front, even though concentrations of reduced rock matrix constituents show little change. Detailed SEM observations revealed that fossilized microorganisms composed of amorphous granules made exclusively of Fe and Si occur in the rock’s pore space. Microbial 16S rDNA analysis suggests that there is presently a zonation of different bacterial groups within the redox band, and bacterial zonation played an important role in the concentration of Fe-oxyhydroxides at the redox front. These water–rock–microbe interactions can be considered analogous to the processes occurring in the redox fronts that would develop around geological repositories for radioactive waste. Once formed, the Fe-oxyhydroxides within such a front would be preserved even after reducing conditions resume following repository closure.