Vocational college students often exhibit low motivation and suboptimal performance in physical fitness activities, negatively affecting both physical health and psychological well‑being. This study examines whether integrating a mindfulness-based intervention (MBI) into the physical education (PE) curriculum can enhance students' physical performance, intrinsic motivation, and emotional regulation during exercise. A mixed-methods empirical design was employed. First-year students from a vocational college in eastern China, facing mandatory physical fitness tests, were assigned to either a mindfulness-integrated group (MI, n = 300) or a waiting-list group (WL, n = 300) based on their classes. The MI group received an eight-week MBI, embedding mindfulness tasks such as mindful breathing, mindful stretching, and challenging exercises during and after PE classes. Pre- and post-intervention measures included standardized physical fitness tests, the Five Facet Mindfulness Questionnaire, the Intrinsic Motivation Inventory, the Distress Tolerance Scale, and the WHO‑5 Well‑Being Index. Compared to the WL group, the MI group was expected to show significant improvements in fitness test scores, mindfulness, intrinsic motivation, distress tolerance, and overall well-being. Interaction effects were anticipated, with students initially lower in mindfulness or intrinsic motivation showing greater gains in fitness performance and well-being. A pilot study using the same design (MI, n = 10; WL, n = 10) indicated overall improvements in fitness outcomes and more positive feedback about PE classes in the MI group. These preliminary findings highlight the potential value of integrating mind-body approaches into physical fitness activities. By enhancing intrinsic motivation and distress tolerance, embedding MBI in PE may be an effective strategy to simultaneously improve students' physical performance and psychological well-being. Future research should explore MBI effects across different majors and investigate mechanisms across various sports activities.