Evidence regarding the effectiveness of mindfulness based interventions (MBIs) for eating disorders, weight management and food craving is emerging and further studies are required to understand the underlying mechanisms of MBIs in these domains. The current study was designed to establish the role of specific mechanisms underlying the putative relationship between mindfulness and reward motivated eating. We predicted that mindfulness would be negatively related to features of reward motivated eating and that this association would be mediated by emotion regulation and habitual negative self-thinking. A cross-sectional survey measuring uncontrolled and emotional eating, mindfulness, emotion regulation and habitual negative self-thinking was completed by female and male meditators and non-meditators (N = 632). Lower levels of dispositional mindfulness were associated with difficulties in emotion regulation, habitual negative self-thinking and both emotional and uncontrolled eating. Difficulties in emotion regulation significantly mediated the mindfulness-uncontrolled eating relationship. Habitual negative self-thinking significantly mediated the mindfulness-emotional eating relationship. Participants with meditation experience reported greater levels of dispositional mindfulness, fewer difficulties with emotion regulation and habitual negative self-thinking and reduced uncontrolled eating tendencies, compared to non-meditators. The findings suggest that MBIs designed to change reward motivated eating and weight control should focus on emotion regulation and mental habits as underlying mechanisms.