This study aimed to identify the factors influencing the food choices of athletes at the Universiade and Commonwealth Games and explore differences in the cohort across sport, competition history and demographic characteristics. A sample of 385 athletes (n = 153, 2017 Universiade, Taiwan; n = 232, 2018 Commonwealth Games, Australia), from 69 countries and 29 sports participated in this cross-sectional observational study. Participants rated 36 items from the Athlete Food Choice Questionnaire and 11 additional items (gut comfort, doping risk, availability, location, money, convenience, time of day, hunger, medical conditions, and food allergies) on how frequently (1 never to 5 always) each influences their food choices. “Performance”, “sensory appeal”, “food and health awareness” and “weight control” were reported as most frequently, while the least were “emotional influence”, “influence of others” and “food values and beliefs”. Commonwealth Games athletes were older, more experienced and more likely to report “performance” (median = 4.33 versus 4.00, U = 20250.0, p = 0.012) and less likely to report “emotional influences” (median = 2.80 versus 3.20, U = 14273.0, p = 0.001) than Universiade athletes. Greater numbers of younger athletes were often or always influenced by available money. Athletes across all sports reported frequently considering gut comfort in their food choices. These results can inform nutrition education strategies of high-performance athletes.