Respiratory and gastrointestinal infections limit an athlete's availability to train and compete. To better understand how sick an athlete will become when they have an infection, a paradigm recently adopted from ecological immunology is presented that includes the concepts of immune resistance (the ability to destroy microbes) and immune tolerance (the ability to dampen defence yet control infection at a non-damaging level). This affords a new theoretical perspective on how nutrition may influence athlete immune health; paving the way for focused research efforts on tolerogenic nutritional supplements to reduce the infection burden in athletes. Looking through this new lens clarifies why nutritional supplements targeted at improving immune resistance in athletes show limited benefits: evidence supporting the old paradigm of immune suppression in athletes is lacking. Indeed, there is limited evidence that the dietary practices of athletes suppress immunity, e.g. low-energy availability and train- or sleep-low carbohydrate. It goes without saying, irrespective of the dietary preference (omnivorous, vegetarian), that athletes are recommended to follow a balanced diet to avoid a frank deficiency of a nutrient required for proper immune function. The new theoretical perspective provided sharpens the focus on tolerogenic nutritional supplements shown to reduce the infection burden in athletes, e.g. probiotics, vitamin C and vitamin D. Further research should demonstrate the benefits of candidate tolerogenic supplements to reduce infection in athletes; without blunting training adaptations and without side effects.