Safe storage of spent nuclear fuel in deep underground repositories necessitates an understanding of the long-term alteration of metal canisters and buffer materials. A small-scale laboratory alteration test was performed on metal (Cu or Fe) chips embedded in compacted bentonite blocks placed in anaerobic water for 1 year. Lactate, sulfate, and bacteria were separately added to the water to promote biochemical reactions in the system. The bentonite blocks immersed in the water were dismantled after 1 year, showing that their alteration was insignificant. However, the Cu chip exhibited some microscopic etch pits on its surface, wherein a slight sulfur component was detected. Overall, the Fe chip was more corroded than the Cu chip under the same conditions. The secondary phase of the Fe chip was locally found as carbonate materials, such as siderite (FeCO3) and calcite ((Ca, Fe)CO3). These secondary products can imply that the local carbonate occurrence on the Fe chip may be initiated and developed by an evolution (alteration) of bentonite and a diffusive provision of biogenic CO2 gas. These laboratory scale results suggest that the actual long-term alteration of metal canisters/bentonite blocks in the engineered barrier could be possible by microbial activities.