Studies on the effects of training confinement on athletes with physical impairments are limited. Hence, in this retrospective cohort study, we aimed to investigate the impact of prolonged cessation of organized team training due to the coronavirus disease 2019 pandemic on the body composition of elite female Japanese basketball athletes. Fourteen female wheelchair basketball athletes (aged ≥20 years) were enrolled. The primary outcomes were lean and adipose indices measured using whole-body dual-energy X-ray absorptiometry. The impact of prolonged organized team training cessation on body composition was investigated by comparing the body composition at baseline and post-training confinement. A reduced whole-body lean mass (p= 0.038) and percent lean mass (p= 0.022), as well as an increased percent body fat (p= 0.035), were observed after the confinement period. The regional analysis revealed reduced percent lean and increased percent fat masses in the trunk (p= 0.015 andp= 0.026, respectively) and upper limbs (p= 0.036 andp= 0.048, respectively). In conclusion, prolonged organized team training cessation reduced lean mass and increased body fat percentage, primarily in the trunk and upper limbs. Individualized training programs targeting these body regions should be implemented to improve body composition and physical conditions in athletes during and after prolonged cessation of organized team training.