Mindfulness-based stress reduction (MBSR) has been proven to improve mental health and quality of life. This study examined how mindfulness training and various types of mindfulness practices altered brain activity. Specifically, the spectral powers of scalp electroencephalography (EEG) of the MBSR group (n = 17) who underwent an 8-week MBSR training-including mindful breathing and body-scan-were evaluated and compared with those of the waitlist controls (n = 14). Empirical results indicated that the long-term intervention effect of MBSR significantly elevated the resting-state beta powers and reduced resting-state delta powers in both practices; such changes were not observed in the waitlist control. Compared with mindful breathing, body-scanning resulted in an overall decline in EEG spectral powers at both delta and gamma bands among trained participants. Together with our preliminary data of expert mediators, the aforementioned spectral changes were salient after intervention, but mitigated along with expertise. Additionally, after receiving training, the MBSR group's Five Facet Mindfulness Questionnaire (FFMQ) and Difficulties in Emotion Regulation Scale (DERS) scores improved significantly, which were correlated with the EEG spectral changes in the theta, alpha, and low-beta bands. This study elaborated the neurophysiological correlates of mindfulness practices, suggesting that MBSR might function as a unique internal processing tool that involves increased vigilant capability and induces alterations similar to other cognitive training. Additionally, the EEG signatures of mindfulness training assessed by this study may serve as objective indicators for evaluating mindfulness practices.