Background Cardiovascular diseases (CVDs) are the leading cause of death in developed countries, significantly affecting quality of life and healthcare costs. While traditional risk factors are well-established, unconventional factors like gut microbiota have gained interest. Understanding the relationship between gut microbiota and cardiovascular events is necessary to enhance current risk stratification strategies. Methods We analyzed data from a local cohort of 500 subjects within the CV-PREVITAL study, a multicentre trial comparing an mHealth intervention with usual care to reduce cardiovascular risk among 28,000 Italian patients over 45 years old. Data included clinical assessments (traditional risk factors, carotid and femoral artery ultrasounds, medical history, anthropometrics) and questionnaires (sleep quality, occupational status, diet, physical activity). Gut microbiota composition was assessed using MetaPhlAn 4 and HUMAnN 3.9, profiling species-level genome bins, gene families, and metabolic pathways. Alpha diversity was analyzed using SGB richness, Shannon, and Simpson indices; beta diversity was evaluated with Bray-Curtis and Jaccard distances. Results Alpha diversity analysis revealed no significant differences between patients with subclinical atherosclerosis and healthy controls. However, beta diversity analysis showed a small but significant separation between these groups, even when patients were stratified by lesion location (femoral artery, carotid artery, or both). Beneficial bacteria such as Oscillibacter sp. ER4 and Anaerostipes hadrus were positively correlated with healthy controls, while unknown Parasutterella SGB0260, Hydrogeniiclostridium mannosilyticum, and unknown SGB14888 were significantly associated with subclinical atherosclerosis. Conclusions Our analysis demonstrated small but significant differences in microbiome composition between patients with subclinical atherosclerosis and healthy controls. Notably, Oscillibacter sp. negatively correlated with blood triglycerides, and Anaerostipes hadrus was enriched in controls adhering to a healthier lifestyle. These findings suggest that incorporating gut microbiota profiles into personalized cardiovascular disease prevention strategies may improve individual risk stratification, potentially reducing CVD morbidity and mortality.