Background: Metabolic syndrome (MetS) is a cluster of metabolic disorders associated with an increased risk of cardiovascular disease (CVD). Post-acute coronary syndrome (ACS) patients with MetS experience worse prognosis and functional recovery. Exercise-based cardiac rehabilitation (CR) is a cornerstone intervention that has shown benefits in reducing cardiovascular risk factors and improving metabolic parameters. Objective: This study aimed to investigate the effects of a supervised 12-week CR program on MetS parameters among patients recovering ACS, in comparison with standard guideline-directed medical therapy alone. Patients and methods: This prospective observational cohort study was performed at Ain Shams University Hospitals between July and December 2021. The study enrolled 62 patients diagnosed with MetS following ACS. Participants were allocated into two groups: Group A (n = 32) underwent supervised exercise-based CR, while group B (n = 30) received standard medical therapy alone. Assessments conducted at baseline and after the intervention period included waist circumference (WC), fasting blood sugar (FBS), triglycerides (TG), high-density lipoprotein cholesterol (HDL-C), and blood pressure (BP). Results: After completing 12 weeks, group A showed marked improvements, characterized by significant decreases in WC by 5.38 cm (P < 0.001), FBS by 14 mg/dL (P = 0.012), and TG levels by 20.5 mg/dL (P = 0.008), accompanied by a notable elevation in HDL-C by 3.5 mg/dL (P = 0.049). BP did not change significantly. In contrast, group B demonstrated no meaningful enhancement in MetS-related parameters. Conclusion: A 12-week supervised exercise-based CR program significantly improved key MetS parameters in post-ACS patients compared to medical therapy alone. These findings underscored the importance of structured CR programs in reducing cardiovascular risks associated with MetS.