Abstract Aim This study aimed to investigate the long-term effects of two exercise-based CR programs on physical activity (PA), sedentary behavior, physical fitness, quality of life (QoL), and mental health in coronary artery disease (CAD) patients. Subject and methods Seventy-two CAD participants were randomized (1:1:1) into HIIT, MICT, and control groups. Both training programs spanned 6 weeks with three supervised treadmill exercise sessions per week. MICT targeted ≈70–75% of peak heart rate (HR), while HIIT aimed for ≈85–95% of peak HR. The control group adhered to standard medical recommendations. Assessments at 6- and 12-months post-intervention included body composition, aerobic capacity, muscle strength, PA, SB, QoL, anxiety, and depression. Results Over the 6- and 12-month follow-up periods, both exercise groups maintained the levels of aerobic capacity (HIIT ≈ 19.6 ml kg−1 min−1, MICT ≈ 17.8 ml kg−1 min−1), QoL, and PA compared to baseline (p < .001). Symptoms of anxiety and depression remained lower than baseline (p < .001). The HIIT group demonstrated a significant decreasing trend in waist circumference (∆m3−m2% −2 cm, p = .033) compared to MICT (p = .016) and control (p = .001) at 6 months of follow-up. It was maintained at 12 months of follow-up with significant differences to MICT (p = .018) and control (p = .001). In contrast, the control group experienced deteriorations in body composition, SB, symptoms of anxiety, and depression, along with a decline in aerobic capacity over time. Conclusion Encouraging CAD patients to maintain elevated PA levels can promote cardiovascular, WC, and mental health. CR exercise programs can reduce cardiovascular risk factors and induce favorable lifestyle changes. Notably, HIIT demonstrated sustained improvements surpassing those of MICT. These findings underscore the importance of structured exercise-based CR programs in optimizing long-term outcomes for CAD patients. Trial Registration https://clinicaltrials.gov/ct2/show/NCT03538119 on May 25, 2018.