Previous work documented the general antibacterial mechanism of iron containing clays that involved hydroxyl radical (•OH) production from soluble Fe2+, and attack of cell membrane and intracellular proteins. Here we explore the role of clay structural Fe(II) in •OH production at near neutral pH and identify a lipid involved in the antibacterial process. Structural Fe(III) in nontronite NAu-2 was reduced (rNAu-2) and E. coli, a model bacterium, was exposed to rNAu-2 in oxic suspension. The antibacterial activity of rNAu-2 was dependent on pH and Fe(II) concentration, where E. coli were completely killed at pH 6, but survived at pH 7 and 8. In the presence of a •OH scavenger or in anaerobic atmosphere, E. coli survived better, suggesting that cell death may be caused by •OH generated from oxidation of structural Fe(II) in rNAu-2. In-situ imaging revealed damage of a membrane lipid, cardiolipin, in the polar region of E. coli cells, where reactive oxygen species and redox-active labile Fe were enriched. Our results advance the previous antibacterial model by demonstrating that the structural Fe(II) is the primary source of •OH, which damages cardiolipin, triggers the influx of soluble Fe2+ into the cell, and ultimately leads to cell death.