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Abstract Objective. Neural signals in residual muscles of amputated limbs are frequently decoded to control powered prostheses. Yet myoelectric controllers assume muscle activity of residual muscle is similar to that of intact muscle. This study sought to understand potential changes to motor unit (MU) properties after limb amputation. Approach. Six people with unilateral transtibial amputation were recruited. Surface electromyogram (EMG) of residual and intact tibialis anterior (TA) and gastrocnemius (GA) muscles were recorded while subjects traced profiles targeting up to 20 and 35% of maximum activation for each muscle (isometric for intact limbs). EMG was decomposed into groups of motor unit (MU) spike trains. MU recruitment thresholds, action potential amplitudes (MU size), and firing rates were correlated to model Henneman’s size principle, the onion-skin phenomenon, and rate-size associations. Organization (correlation) and modulation (rates of change) of relations were compared between intact and residual muscles. Main results. The residual TA exhibited significantly lower correlation and flatter slopes in the size principle and onion-skin, and each outcome covaried between the MU relations. The residual GA was unaffected for most subjects. Subjects trained prior with myoelectric prostheses had minimally affected slopes in the TA. Rate-size association correlations were preserved, but both residual muscles exhibited flatter decay rates. Significance. We showed peripheral neuromuscular damage also leads to spinal-level functional reorganization. Our findings suggest models of MU recruitment and discharge patterns for residual muscle EMG generation need reparameterization to account for disturbances observed. In the future, tracking MU pool adaptations may also provide a biomarker of neuromuscular control to aid training with myoelectric prostheses.