A healthy lifestyle is based on a correct diet and regular exercise. Little is known about the effect of different types of exercise on dietary preferences. To address the question of whether high-intensity interval training (HIIT) could modulate spontaneous food choices, an experimental study was carried out on 32 young, healthy normal-weight subjects. The spontaneous diet of each subject has been monitored over nine weeks of indoor-cycling training, divided into three mesocycles with an incremental pattern: total energy intake, macronutrients and micronutrients have been analysed. A two-way mixed model has been used to assess differences in dietary variables; a principal factor analysis has been performed to identify sample subgroups. An increased energy intake (+17.8% at T3; p < 0.01) has been observed, although macronutrients’ proportions did not vary over time, without differences between sexes. An increase of free fat mass was found in the last mesocycle (+3.8%), without an augmentation of body weight, when, despite the increased training load, a stabilization of energy intake occurred. Three different subgroups characterized by different dietary modifications could be identified among participants that showed a common trend towards a healthier diet. Nine weeks of HIIT promoted a spontaneous modulation of food choices and regulation of dietary intake in young normal-weight subjects aged 21–24. Importantly, this life-period is critical to lay the foundation of correct lifestyles to prevent metabolic diseases and secure a healthy future with advancing age.