Mindfulness is assumed to foster the ability to consistently act in line with one’s authentic self; a skill which has been found to enhance students’ autonomous motivated behavior in the educational context. However, evidence regarding how mindfulness can be integrated into existing conceptual frameworks such as the trans-contextual model is scarce. Therefore, the present study aimed to evaluate the role of mindfulness in students’ autonomous motivation in the school and leisure time contexts. Overall, N = 1877 students (M = 14.74 years, SD = 2.63) indicated their self-reported mindfulness, their perceived need for support in physical education, their autonomous motivation during physical education and leisure time, as well as their perceived behavioral control, attitude, subjective norm, and intention toward physical activity. Physical activity was additionally measured physiologically for n = 240 students using accelerometers. Path model analyses revealed that the inclusion of mindfulness substantially improved the trans-contextual model fit. Perceived autonomy support positively predicted mindfulness, which, in turn, predicted autonomous motivation in physical education and leisure time, attitude, subjective norm, and perceived behavioral control. Furthermore, mediation analyses revealed the significant indirect effects of mindfulness on physiological and self-reported physical activity. Based on these results, mindfulness can be considered a key factor in fostering students’ motivation to become physically active.