Methionine restriction (MR) has been shown to affect mitochondrial function including altering oxygen consumption, reactive oxygen species (ROS) generation, Complex expression, and oxidative damage. The sulfur-containing amino acid methionine can become oxidized forming methionine sulfoxide which can lead to changes in protein function and signaling. Methionine sulfoxide reductases are endogenous enzymes capable of reducing methionine sulfoxide, with Methionine sulfoxide reductase A (MsrA) being ubiquitously expressed in mammals. Here we investigated if the effects of MR on mitochondrial function required functional MsrA in the liver and kidney which are the major tissues involved in sulfur biochemistry and both highly express MsrA. Moreover, MsrA is endogenously found in the mitochondria thereby providing potential mechanisms linking diet to mitochondrial phenotype. We found sex-specific changes in oxygen consumption of isolated mitochondria and females showed changes with MR in a tissue-dependent manner – increased in liver and decreased in kidney. Loss of MsrA increased or decreased oxygen consumption depending on the tissue and which portion of the electron transport chain was being tested. In general, males had few changes in either tissue regardless of MR or MsrA status. Hydrogen peroxide production was increased in the kidney with MR regardless of sex or MsrA status. However, in the liver, production was increased by MR in females and only slightly higher with loss of MsrA in both sexes. Mitochondrial Complex expression was found to be largely unchanged in either tissue suggesting these effects are driven by regulatory mechanisms and not by changes in expression. Together these results suggest that sex and MsrA status do impact the mitochondrial effects of MR in a tissue-specific manner.