Brain-computer interfaces (BCIs) are promising tools for assisting patients with paralysis, but suffer from long training times and variable user proficiency. Mind-body awareness training (MBAT) can improve BCI learning, but how it does so remains unknown. Here we show that MBAT allows participants to learn to volitionally increase alpha band neural activity during BCI tasks that incorporate intentional rest. We trained individuals in mindfulness-based stress reduction (MBSR; a standardized MBAT intervention) and compared performance and brain activity before and after training between randomly assigned trained and untrained control groups. The MBAT group showed reliably faster learning of BCI than the control group throughout training. Alpha-band activity in EEG signals, recorded in the volitional resting state during task performance, showed a parallel increase over sessions, and predicted final BCI performance. The level of alpha-band activity during the intentional resting state correlated reliably with individuals' mindfulness practice as well as performance on a sustained attention task. Collectively, these results show that MBAT modifies a specific neural signal used by BCI. MBAT, by increasing patients' control over their brain activity during rest, may increase the effectiveness of BCI in the large population who could benefit from alternatives to direct motor control.