Objective: Brain-computer interfaces (BCIs) constitute a promising tool for communication and control. However, mastering non-invasive closed-loop systems remains a learned skill that is difficult to develop for a non-negligible proportion of users. The involved learning process induces neural changes associated with a brain network reorganization that remains poorly understood. Approach: To address this inter-subject variability, we adopted a multilayer approach to integrate brain network properties from electroencephalographic (EEG) and magnetoencephalographic (MEG) data resulting from a four-session BCI training program followed by a group of healthy subjects. Our method gives access to the contribution of each layer to multilayer network that tends to be equal with time. Main results: We show that regardless the chosen modality, a progressive increase in the integration of somatosensory areas in the α band was paralleled by a decrease of the integration of visual processing and working memory areas in the β band. Notably, only brain network properties in multilayer network correlated with future BCI scores in the α 2 band: positively in somatosensory and decision-making related areas and negatively in associative areas. Significance: Our findings cast new light on neural processes underlying BCI training. Integrating multimodal brain network properties provides new information that correlates with behavioral performance and could be considered as a potential marker of BCI learning.