Balance training programs have been shown to reduce ankle sprain injuries in sports, but little is known about the transfer from this training modality to motor coordination and ankle joint biomechanics in sport-specific movements. This study aimed to investigate the effects of wobble board training on motor coordination and ankle mechanics during early single-leg landing from a lateral jump. Twenty-two healthy men were randomly assigned to either a control or a training group, who engaged in 4 weeks of wobble board training. Full-body kinematics, ground reaction force, and surface electromyography (EMG) from 12 lower limb muscles were recorded during landing. Ankle joint work in the sagittal, frontal, and transverse plane was calculated from 0 to 100 ms after landing. Non-negative matrix factorization (NMF) was applied on the concatenated EMG Pre- and Post-intervention. Wobble board training increased the ankle joint eccentric work 1.2 times in the frontal (P < .01) and 4.4 times in the transverse plane (P < .01) for trained participants. Wobble board training modified the modular organization of muscle recruitment in the early landing phase by separating the activation of plantar flexors and mediolateral ankle stabilizers. Furthermore, the activation of secondary muscles across motor modules was reduced after training, refocusing the activation on the main muscles involved in the mechanical main subfunctions for each module. These results suggest that wobble board training may modify motor coordination when landing from a lateral jump, focusing on the recruitment of specific muscles/muscle groups that optimize ankle joint stability during early ground contact in single-leg landing.