Background: Spinal cord injury (SCI) is a central nervous system injury that often leads to motor, sensory and autonomic dysfunction. Non-invasive trans-spinal electrical stimulation (ts-ES) has been shown to activate neural networks below the injury and improve motor function recovery after SCI. The objective of this study was to compare changes in motor and autonomic function attributable to ts-ES in individuals with incomplete SCI after 4 weeks of personalized training. Methods: Participants received 4 weeks of treadmill training with personalized step-cycle based PNS and FES with and without non-invasive lumbar ts-ES. Clinical outcome measures of motor function (2-minute walk test, Berg Balance and modified SCIM-Mobility) and metabolic analysis (heart rate and rate of oxygen consumption (VO2 sub-max)) were assessed before and after training. Non-invasive electromyography (EMG) and kinematic data assessed motor function. Results: Based on participant feedback and data, ts-ES with PNS/FES during training was tolerable, improved leg movement and facilitated muscle activity in knee extensors with 10-25% increased RMS amplitude of pre-training EMG activity during both forward and backward walking. Moreover, ts-ES tended to increase HR and VO2 sub-max within one session. Conclusions: Personalized rehabilitation strategies combining ts-ES with traditional physiotherapy exercises and locomotor training have the potential to improve recovery after SCI.