Objectives <p>Many meditation practices use the breath as an attentional anchor, and this may naturally slow respiration. However, it remains unclear whether intentionally slowing the breath during mindfulness meditation produces effects beyond those of spontaneous breathing. This study examined the effects of naturally occurring versus intentional slow breathing during mindfulness meditation on neural oscillations and sympathetic arousal.</p> Method <p>In a single experimental session, participants were randomly assigned to one of two mindfulness meditation conditions: spontaneous breathing (<i>n</i> = 40; <i>M</i>_age = 20.2; 32 females) or paced breathing (<i>n</i> = 40; <i>M</i>_age = 19.8; 30 females). Electroencephalography (EEG) and skin conductance level (SCL) were recorded <i>before</i>, <i>during</i>, and <i>after</i> mindfulness meditation. Global amplitudes were assessed across the five traditional EEG frequency bands.</p> Results <p>Respiratory rate decreased more from <i>before</i> to <i>during</i> in paced breathing than in spontaneous breathing. Compared with spontaneous breathing, paced breathing resulted in a larger increase in theta (4–7.5&#xa0;Hz) amplitude and a smaller decrease in alpha (8–13&#xa0;Hz) amplitude from <i>before</i> to <i>during</i>. Additionally, beta (13.5–30&#xa0;Hz) amplitude and SCL increased from <i>befor</i>e to <i>during</i> in paced breathing but decreased in spontaneous breathing.</p> Conclusions <p>Intentional slow breathing during mindfulness meditation differentially affects neural oscillations and sympathetic arousal, consistent with an effect of breath pacing on attentional and arousal processes. These findings suggest that breath control may shape the psychophysiological effects of mindfulness meditation, with potential implications for well-being and for the treatment of psychological disorders.</p> Preregistration <p>This study is not preregistered.</p>