The effect of selected phenolic-containing beers (pale lager, barley wine, tripel), white wine, and red wine on the formation of lipid oxidation products (thiobarbituric acid reactive substances, 4-hydroxy-2-hexenal, 4-hydroxy-2-nonenal) and protein carbonylation during simulated gastrointestinal digestion of pork and salmon was investigated. Greater antioxidant effects of the beverages were observed during the digestion of salmon, whereas antioxidant effects were less pronounced or absent during the digestion of pork. Red wine contained the highest levels of phenolics, accompanied by the highest antioxidant effects among the beverages tested. Secondly, the simultaneous formation of potentially harmful fatty acid ethyl esters (FAEEs) was observed for the first time when these muscle foods were digested with the beers and wines tested, or with pure ethanol. These FAEEs were formed by lipase activity in the presence of ethanol, which was blocked by the lipase inhibitor orlistat. The formation of selected FAEEs corresponded well with the levels of their precursor fatty acids in muscle, resulting in different FAEE profiles in the digests of chicken, pork, beef, or salmon with ethanol. In conclusion, the formation of potentially harmful FAEE may counteract the observed beneficial antioxidant effects of phenolic-rich alcoholic beverages during the gastrointestinal digestion of muscle foods.