We have previously evidenced that Mindfulness Meditation (MM) in experienced meditators (EMs) is associated with long-lasting topological changes in resting state condition. However, what occurs during the meditative phase is still debated. Utilizing magnetoencephalography (MEG), the present study is aimed at comparing the topological features of the brain network in a group of EMs (n = 26) during the meditative phase with those of individuals who had no previous experience of any type of meditation (NM group, n = 29). A wide range of topological changes in the EM group as compared to the NM group has been shown. Specifically, in EMs, we have observed increased betweenness centrality in delta, alpha, and beta bands in both cortical (left medial orbital cortex, left postcentral area, and right visual primary cortex) and subcortical (left caudate nucleus and thalamus) areas. Furthermore, the degree of beta band in parietal and occipital areas of EMs was increased too. Our exploratory study suggests that the MM can change the functional brain network and provides an explanatory hypothesis on the brain circuits characterizing the meditative process.