Microbial iron reduction (MIR) is an important and ubiquitous natural process in the biogeochemical cycling of iron and carbon in anaerobic sedimentary and subsurface environments. The objectives of this study were (1) to determine if the MIR process can enhance the inactivation of Escherichia coli cells under anaerobic conditions and (2) to identify potential inactivation mechanisms. Laboratory microcosm experiments showed that the presence of MIR activity significantly enhanced E. coli inactivation, and the inactivation rate under the MIR condition was significantly larger than those under other anaerobic redox conditions. Under anoxic condition, higher Fe²⁺concentrations exhibited a linear function to larger E. coli inactivation rates, indicating that the production of Fe²⁺by MIR was one of the important roles in E. coli inactivation. When E. coli cells were amended as the sole electron source to the MIR process, increased Fe²⁺ production was observed, which corresponded to decreasing TOC concentration. Together, the results suggest that MIR enhanced E. coli inactivation through the production of Fe²⁺ as a metabolic waste, and the inactivation benefited the MIR process as the inactivated cells were used as an electron source, which represents a potential new mechanism for bacterial inter-species competition. This knowledge could further improve our understanding of the fate of fecal bacteria in natural environments where the MIR process is prevalent, and may also be explored for enhanced removal of bacterial pathogens in engineering processes.