The practice of physical activity and adherence to the Mediterranean diet (AMD) have been extensively studied for their relationship with kinanthropometric, body composition and physical fitness variables. However, no previous study has analyzed whether these healthy habits are equally determinant for the differences found in kinanthropometric, body composition and physical fitness variables or, on the contrary, if one of them is more relevant. For this reason, the objectives of the present study were: (1) to analyze the differences in kinanthropometric, body composition, and physical fitness variables between adolescents with different levels of physical activity and AMD, and (2) to determine whether physical activity and/or AMD are predictors of differences in kinanthropometric variables, body composition or physical fitness in adolescents. The sample consisted of 791 adolescents (404 males and 387 females; mean age: 14.39±1.26 year-old) whose physical activity level, AMD, kinanthropometric variables, body composition and physical fitness, were measured. The results showed differences when considering the level of physical activity in kinanthropometric variables, body composition and physical fitness, but not the level of AMD, which was relevant only when it was poor, and the adolescents were inactive. Nevertheless, the AMD did not seem to exert such a determining effect as to produce significant differences on its own. On the other hand, the practice of physical activity did act as a predictor mainly of changes in the fitness variables. Therefore, the main novelty of the present study is the establishment of an order of importance of the healthy habits acquired by adolescents, concluding that the practice of physical activity is more determinant for the differences found in the study variables.