Sedentary behaviours in adults with intellectual disabilities (ID) negatively impact health-related determinants and increase the risk of physical dysfunction or chronic health issues. Inclusive sport practice can enhance social inclusion and fitness, benefiting overall person development and life quality. This study aimed to assess fitness level variation in athletes with and without ID before and after a 9-month inclusive (INC) and non-inclusive (N_INC) basketball training. 38 athletes with ID and 14 athletes without ID belonged to INC group, 38 athletes with ID belonged to N_INC group and 23 participants with ID belonged to the control group (CG). Before and after the intervention period, all participants performed anthropometric (body weight, body mass index, body fat percentage) and fitness tests (muscle strength and power, cardiovascular endurance, balance, flexibility, agility, movement speed, and coordination). ID and non-ID athletes of both INC and N_INC groups significantly improved in most of the tests (weight, balance, flexibility, muscle strength, endurance, agility, movement speed and coordination) while CG group significantly worsened weight, muscle endurance, flexibility, agility, movement speed and coordination, after the intervention (p < 0.05). These findings showed that sport training improved fitness in athletes with ID, decreasing health risks. Moreover, involving in the same training group persons with and without disabilities, does not limit the beneficial effects that training induce on persons without ID and could be a valid way to promote both social inclusion and physical health of persons with ID.