An early event that occurs in response to alcohol consumption is mitochondrial dysfunction, which is evident in changes to the mitochondrial proteome, respiration defects, and mtDNA damage. S-Adenosylmethionine (SAM) has emerged as a potential therapeutic for treating alcoholic liver disease through mechanisms that appear to involve decreases in oxidative stress and pro-inflammatory cytokine production, as well as alleviation of steatosis. Because mitochondria are a source of reactive oxygen/nitrogen species and target for oxidative damage we tested the hypothesis that SAM treatment during alcohol exposure preserves organelle function. Mitochondria were isolated from livers of rats fed control and ethanol diets with and without SAM for 5 weeks. Alcohol feeding caused a significant decrease in State 3 respiration and respiratory control ratio, whereas SAM administration prevented these alcohol-mediated defects and preserved hepatic SAM levels. SAM treatment prevented alcohol-associated increases in mitochondrial superoxide production, mtDNA damage, and iNOS induction, without a significant lessening of steatosis. Accompanying these indices of oxidant damage, SAM prevented alcohol-mediated losses in cytochrome c oxidase subunits as shown using BN-PAGE proteomics and immunoblotting, which resulted in partial preservation of complex IV activity. SAM treatment attenuated the upregulation of the mitochondrial stress chaperone prohibitin. Although SAM supplementation did not alleviate steatosis by itself, SAM prevented several key alcohol-mediated defects to the mitochondria genome and proteome that contribute to the bioenergetic defect in liver following alcohol consumption. These findings reveal new molecular targets through which SAM may work to alleviate one critical component of alcohol-induced liver injury, mitochondria dysfunction.