Increasing consumption of cereals has been associated with reduced risk of several chronic diseases, as they contain phytochemicals that combat oxidative stress. Cereal contamination by the “emerging mycotoxins” beauvericin (BEA) and enniatins (ENs) is a worldwide health problem that has not yet received adequate scientific attention. Their presence in feeds represents a risk for animals and a potential risk for humans because of their carry-over to animal-derived products. This preliminary study aimed to investigate if the total antioxidant capacity (TAC) of corn, barley, and wheat flours could be influenced by contamination with increasing levels of BEA and ENN B. The highest TAC value was observed in barley compared with wheat and corn (p < 0.001) before and after contamination. No effect of mycotoxin or mycotoxin level was found, whereas cereal x mycotoxin exhibited a significant effect (p < 0.001), showing a lower TAC value in wheat contaminated by ENN B and in barley contaminated by BEA. In conclusion, barley is confirmed as a source of natural antioxidants with antiradical potentials. Additional studies with a larger sample size are necessary to confirm the obtained results, and investigations of the toxic effects of these emergent mycotoxins on animals and humans should be deepened.