Spinal Cord Injury (SCI) leads to significant motor deficits, but is often incomplete with spared fibers across the lesion and intact sensory feedback reaching the spinal circuits. This study seeks to enhance the integration of residual supraspinal commands with spinal-level sensory input to improve motor function by inducing adaptive plasticity within the neuronal networks below the site of injury. To selectively increase the supraspinal locomotor drive, we targeted the cuneiform nucleus (CnF) using viral vector delivery of optogenetic activators in a thoracic incomplete SCI mouse model. Physical therapy was implemented to facilitate functional recovery below the lesion site. Locomotor behavioral profiling was used to quantify short and long-term recovery of motor function effects in animals undergoing physical therapy and/or optical stimulation. By temporally aligning CnF stimulation with sensory feedback activation driven by physical therapy, we optimized a close-loop stimulation, the NeuroLoop protocol. Monitoring muscle activity during stimulation revealed that sensory driven activation of intrinsic spinal locomotor networks was a prerequisite to promote potentiation of the remaining and optically activated descending locomotor signal. Therefore, optimal recovery of function occurred when peripheral sensory inputs (proprioceptive and tactile) were integrated in a timely manner with the descending CnF motor commands in the spinal cord below the injury site. In conclusion, these findings underscore the efficacy of CnF close-loop stimulation in combination with appropriate physical therapy to promote motor recovery post-SCI and introduces the NeuroLoop protocol as a personalized treatment to restore motor control after SCI.