Motor coordination and lower limb biomechanics are crucial aspects of anterior cruciate ligament (ACL) injury prevention strategies in football. These two aspects have never been assessed together in real scenarios in the young population. The present study aimed to investigate the influence of motor coordination on lower limb biomechanics in young footballers during an on-the-pitch training. Eighteen juvenile football players (10 y ± 2 m) were enrolled. Each player performed a training drill with sport-specific movements (vertical jump, agility ladders, change of direction) and the Harre circuit test (HCT) to evaluate players' motor coordination. Wearable inertial sensors (MTw Awinda, Xsens) were used to assess lower limb joint angles and accelerations. Based on the results of the HCT, players were divided into poorly coordinated (PC) and well-coordinated (WC) on the basis of the literature benchmark. The PC group showed a stiffer hip biomechanics strategy (up to 40% lower flexion angle, ES = 2.0) and higher internal-external hip rotation and knee valgus ( < 0.05). Significant biomechanical limb asymmetries were found only in the PC group for the knee joint (31-39% difference between dominant and non-dominant limb, ES 1.6-2.3). Poor motor coordination elicited altered hip and knee biomechanics during sport-specific dynamic movements. The monitoring of motor coordination and on-field biomechanics might enhance the targeted trainings for ACL injury prevention.