Numerous athletes compete at a high level without consuming animal products; although a well-planned vegan diet might be appropriate for all stages of the life cycle, a few elements need to be addressed to build a balanced plant-based diet for an athlete, particularly in bodybuilding, in which muscle growth should be maximised, as athletes are judged on their aesthetics. In this observational study, nutritional intakes were compared in a cohort of natural omnivorous and vegan bodybuilders, during two different phases of preparation. To this end, 18 male and female bodybuilders (8 vegans and 10 omnivores) completed a food diary for 5 days during the bulking and cutting phases of their preparation. A mixed-model analysis was used to compare macro- and micronutrient intakes between the groups in the two phases. Both vegans and omnivores behaved similarly regarding energy, carbohydrate, and fat intakes, but vegans decreased their protein intake during the cutting phase. Our results suggest that vegan bodybuilders may find difficulties in reaching protein needs while undergoing a caloric deficit, and they might benefit from nutritional professionals' assistance to bridge the gap between the assumed proteins and those needed to maintain muscle mass through better nutrition and supplementation planning.