Metabolic syndrome (MetS) increases the risk of cardiovascular disease, type 2 diabetes mellitus, and cancer. Despite the higher prevalence of MetS in obese adults, little is known about the effectiveness of intensive and group interventions in improving MetS prevalence. This study aimed to investigate the effectiveness of an intensive lifestyle program in reducing the prevalence of MetS in adults with obesity. Patients with obesity (n = 456, 48.8 12.8 years, 18.5% male) were randomized in two groups as indicated in a prospective interventional real-life study: a control group (CG), in which patients received usual care, and an interventional group (IG), in which the patients participate in a healthy lifestyle habits program in six weekly sessions, IGOBE program. Anthropometric, body composition, medications, and MetS features data were analyzed in both groups at the pre-intervention and post-intervention stages using a completer’s analysis. At 12 months of follow-up, the IG showed a relative reduction of 13.4% in the prevalence of MetS from baseline, while the CG showed a reduction of 2.1% (p < 0.001). A significant reduction was also observed in four of five MetS features. In this trial, implementation of the IGOBE program resulted in a significant reduction in MetS prevalence and better control of MetS features compared with the standard of care.