Brain–machine interfaces (BMI) permit bypass motor system disruption by coupling contingent neuroelectric signals related to motor activity with prosthetic devices that enhance afferent and proprioceptive feedback to the somatosensory cortex. In this study, we investigated neural plasticity in the motor network of severely impaired chronic stroke patients after an EEG-BMI-based treatment reinforcing sensorimotor contingency of ipsilesional motor commands. Our structural connectivity analysis revealed decreased fractional anisotropy in the splenium and body of the corpus callosum, and in the contralesional hemisphere in the posterior limb of the internal capsule, the posterior thalamic radiation, and the superior corona radiata. Functional connectivity analysis showed decreased negative interhemispheric coupling between contralesional and ipsilesional sensorimotor regions, and decreased positive intrahemispheric coupling among contralesional sensorimotor regions. These findings indicate that BMI reinforcing ipsilesional brain activity and enhancing proprioceptive function of the affected hand elicits reorganization of contralesional and ipsilesional somatosensory and motor-assemblies as well as afferent and efferent connection–related motor circuits that support the partial re-establishment of the original neurophysiology of the motor system even in severe chronic stroke.