– Objective: the use of motor imagery (MI) in motor rehabilitation protocols has been increasingly investigated as a potential technique for enhancing traditional treatments, yielding better clinical outcomes. However, since MI performance can be challenging, practice is usually required. This demands appropriate training, actively engaging the MI-related brain areas, consequently enabling the user to properly benefit from it. The role of feedback is central for MI practice. Yet, assessing which underlying neural changes are feedback-specific or purely due to MI practice is still a challenging effort, mainly due to the difficulty in isolating their contributions. In this work, we aimed to assess functional connectivity (FC) changes following MI practice that are either extrinsic or specific to feedback. Approach: to achieve this, we investigated FC, using graph theory, in electroencephalography (EEG) and functional magnetic resonance imaging (fMRI) data, during MI performance and at resting-state (rs), respectively. Thirty healthy subjects were divided into three groups, receiving no feedback (control), “false” feedback (sham) or actual neurofeedback (active). Participants underwent 12 to 13 hands-MI EEG sessions and pre- and post-MI training fMRI exams. Main results: following MI practice, control participants presented significant increases in degree and in eigenvector centrality for occipital nodes at rs-fMRI scans, whereas sham-feedback produced similar effects, but to a lesser extent. Therefore, MI practice, by itself, seems to stimulate visual information processing mechanisms that become apparent during basal brain activity. Additionally, only the active group displayed decreases in inter-subject FC patterns, both during MI performance and at rs-fMRI. Significance: hence, actual neurofeedback impacted FC by disrupting common inter-subject patterns, suggesting that subject-specific neural plasticity mechanisms become important. Future studies should consider this when designing experimental NFBT protocols and analyses.