Objectives: Contralesional brain connectivity plasticity was previously reported after stroke. This study aims at disentangling the biological mechanisms underlying connectivity plasticity in the uninjured motor network after an ischemic lesion. In particular, we measured generalized fractional anisotropy (GFA) and magnetization transfer ratio (MTR) to assess whether post-stroke connectivity remodeling depend on axonal and/or myelin changes. Materials and Methods: Diffusion Spectrum Imaging (DSI) and Magnetization Transfer MRI at 3T were performed in 10 patients in acute phase, at one and six months after stroke, which was affecting motor cortical and/or subcortical areas. Ten age- and gender- matched healthy volunteers were scanned one month apart for longitudinal comparison. Clinical assessment was also performed in patients prior to MRI. In the contra-lesional hemisphere, average measures and tract-based quantitative analysis of GFA and MTR was performed to assess axonal integrity and myelination along motor connections as well as their variations in time. Results and Conclusions: Mean and tract-based measures of MTR and GFA showed significant changes in a number of contralesional motor connections, confirming both axonal and myelin plasticity in our cohort of patients. Moreover, density-derived features (peak height, standard deviation-SD and skewness) of GFA and MTR along the tracts showed additional correlation with clinical scores than mean values. These findings reveal the interplay between contralateral myelin and axonal remodeling after stroke.