Microbial methanogenesis is a major source of atmospheric methane (CH₄), a potent greenhouse gas. Therefore, elucidating the metabolic regulatory mechanisms of methanogens is essential for mitigating global warming. Clay minerals represent one of the crucial iron reservoirs in natural environments and commonly coexist with methanogens. Although Fe(III)-rich clay minerals are known to inhibit methanogenic activity, the precise mechanisms underlying this suppression remain poorly understood. To bridge this knowledge gap, a series of cultivation experiments were conducted using a methanogenic archaeon Methanosarcina mazei strain zm-15 in the presence and absence of four different clay minerals with varying iron contents, including nontronite NAu-2, montmorillonite SWy-3 and STx-1b, and kaolinite KGa-1b. Our results revealed that M. mazei strain zm-15 was capable of reducing structural Fe(III) in clay minerals. Among the tested systems, the NAu-2-containing biosystem exhibited the most pronounced iron reduction, which correlated with a significant suppression of methanogenesis. This reduction in CH₄ production was associated with a decline in cell density and slower substrate utilization, indicating that microbial activity was inhibited during the bioreduction of NAu-2. Proteomic analyses further supported these results, revealing the downregulation of key enzymes involved in CH₄ production. The inhibition of methanogenesis was attributed to the release of Fe²⁺ and Al³⁺ ions from the bioreduced NAu-2. These cations exerted a synergistic toxic effect on strain zm-15, as evidenced by experiments exposing the cells to aqueous solutions of Fe²⁺ and/or Al³⁺. In contrast to NAu-2, the other clay minerals tested showed negligible or minimal changes upon microbial iron reduction. However, the bioreduction of NAu-2 led to formation of illite as a secondary mineral. These results provide new insights into the mechanisms by which Fe(III)-rich clay minerals regulate methanogenic activity, emphasizing the role of biogenic cation toxicity in controlling microbial CH₄ production.