The aim of this study is to analyse the relationship between sport modalities practiced, physical fitness, body composition, and healthy habits in an active young population, using a statistical model for prediction. A total of 2255 (1528 boys and 727 girls) children and adolescents aged 6–17 years old who were involved in extracurricular sports from rural areas of Spain participated. Physical fitness was assessed through validated field test and, body composition was determinated using bioelectrical impedance analysis. Adherence to the Mediterranean diet was assessed by KIDMED questionnaire. The general sport variable was significant in VO2max when comparing the invasion and combat modalities to the reference level (court/net). The sex and age variables revealed significant differences in all physical fitness and body composition parameters. Health parameters, such as hours of additional practice, adherence to the Mediterranean diet, and previous experience, showed significant differences. The study concludes that the sport modality variables of training, sex, age, and maturational period have an impact on body composition and fitness parameters in this population. Therefore, by focusing on factors associated with lower values in health indicators, we can prevent health problems during adulthood, such as cardiorespiratory deficits.