Disposal facilities in deep geological formations are considered to be a possible solution for long-term management of high-level nuclear waste (HLW). The design of the repository generally consists of a multiple-barrier system including Fe-based canisters and a clay backfill material. The Fe-clay system will undergo a thermal gradient in time and space, the heat source being the HLW inside the canisters. In the present paper, the effect of a thermal gradient in space on Fe-smectite interactions was investigated. For this purpose, a tube-in-tube experimental device was developed and an 80–300°C thermal gradient was applied to a mixture of MX80 bentonite, metallic Fe (powder and plate), magnetite, and fluid over periods of 1 to 10 months. Transformed and newly formed clay minerals were characterized by scanning electron microscopy, transmission electron microscopy, X-ray diffraction, and Mössbauer spectroscopy. The main mineralogical transformations were similar to those described for batch experiments: smectite was destabilized into an Fe-enriched trioctahedral smectite and Fe-serpentine or chlorite as a function of the experimental conditions. Newly formed clay was observed all along the walls of the gold tube. Their crystal chemistry was clearly different from the clays observed in the hot and cold part of the tubes. The thermal diffusion of elements was also observed, especially that of Mg, which migrated toward the hottest parts of the tubes. In the end, the thermal gradient affected the redox equilibria; more reduced conditions were observed in the hotter parts of the tubes.