Abstract <p>Mindfulness meditation has been suggested to protect mental health and enhance cognitive functions. However, the effectiveness of mindfulness breathing meditation for the general population in Malaysia has not been well documented. This study investigated the effects of mindfulness breathing meditation on perceived stress levels and cognitive functions (i.e., visual attention, inhibitory control, and cognitive flexibility) using heart rate variability (HRV) and eye-tracking methods. Fifty Malaysian adults aged between 18 and 34 years participated in this study. Participants were randomly allocated to either mindfulness breathing meditation or active control (music therapy) groups. Participants underwent a four-week intervention consisting of 30&#xa0;min of online classes once a week and 10&#xa0;min of daily meditation self-practice or music listening. The results showed significant improvement in cognitive flexibility and reduction in perceived stress levels after the intervention in the mindfulness breathing meditation group compared to the active control group. Participants in the mindfulness breathing meditation group self-reported this intervention as highly acceptable and effective in promoting stress reduction, emotional regulation, and attentional control. However, no significant improvement was found in attention, inhibitory control, and HRV after the intervention, suggesting that the mindfulness breathing meditation had no effect on these variables. While short-term engagement with mindfulness breathing meditation practice is achievable, the three-month follow-up using the Mindfulness Adherence Questionnaire showed that sustaining long-term adherence remains a challenge.</p> Protocol registration <p>The approved Stage 1 protocol can be found under “Files”, named “SR_HLY_Manuscript_OSF”, via this link: <a href="https://doi.org/10.17605/OSF.IO/P67EG">https://doi.org/10.17605/OSF.IO/P67EG</a>.</p>