BACKGROUND: The academic development and widespread adoption of meditation practices for well-being and therapy have predominantly focused on secularised adaptations of Buddhist and Hindu techniques. This study aims to expand the field by investigating Christian and Islamic meditation that emphasize the spiritual significance of the heart through elements of visualisation and recitation. It compares the effects of spiritual heart-centred meditation with mindfulness meditation and a waitlist control, focusing on dimensions of social functioning, psychophysiology, cognition, and mental health. METHOD: This study employs a stratified 3-arm randomised controlled method with mixed-method repeated measures across three assessment time points: before intervention (T1), after an 8-week intervention (T2), and at a 3-month follow up (T3). The three conditions include spiritual meditation (either Christian or Islamic), mindfulness meditation (Mindfulness-Based Stress Reduction - MBSR), and a waitlist. Participants will be stratified into Christian and Muslim samples and randomly allocated to the spiritual meditation, MBSR, or waitlist control conditions. Importantly, participants assigned to the spiritual meditation condition will be matched to the spiritual meditation program corresponding to their religion. The intervention will be administered through a mobile phone app with daily 20-minute guided meditation sessions for eight weeks. Primary outcomes pertain to the domain of interpersonal functioning, focusing on prosociality, forgiveness, empathy, and perspective taking. Secondary outcomes include physiology: pain tolerance, pain intensity, stress reactivity assessed via heart rate (HR) and heart rate variability (HRV), psychophysiological reactivity associated with a forgiveness task as measured through HR and HRV, attention (alerting, orienting, and executive attention networks), and mental health (stress, depression, anxiety, subjective well-being, positive and negative affect). DISCUSSION: This trial aims to test the effects of an app-based Christian and Islamic meditation, compared to secular mindfulness and a waitlist, using a randomised controlled trial. If the results yield positive outcomes, this study will support the efficacy of these contemplations, offering practitioners a way to enhance their well-being within their religious framework. TRIAL REGISTRATION: ClinicalTrials.gov, NCT06136676. Registered on 18 November 2023. https://clinicaltrials.gov/study/NCT06136676 .