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Dietary methionine restriction is associated with improved health outcomes and an increase in lifespan in animal models. We have previously shown that an increase in dietary methionine induces alteration in the intestinal microbiome. The composition of the intestinal microbiota is a determinant of health and we, therefore, hypothesized that dietary methionine restriction would also induce changes in the murine microbiome. After one month on a methionine-restricted diet, five-month-old male and female C57BL/6 mice had decreased levels of serum methionine, without changes in body weight. We identified a decrease in the hepatic methylation status of animals fed a methionine-restricted diet compared to controls. This decrease was not associated with changes in DNA or protein methylation in the liver. In males, we saw an increase in families <i>Bacteroidaceae</i> and <i>Verrucoccaceae</i> (mostly <i>A. mucinophila</i>) and a decrease in <i>Rumminococcaceae</i> in animals fed a methionine-restricted diet compared to controls. In females, <i>Bacteroidales</i> family S24-7 was increased two-fold, while families <i>Bacteroidaceae</i>, <i>Verrucoccaceae, Rumminococcaceae,</i> and <i>Rikenellaceae</i> were decreased compared to controls. In summary, feeding a methionine-restricted diet for one month was associated with significant and sex-specific changes in the intestinal microbiome.