Atherosclerotic cardiovascular disease remains a major health issue, often developing silently as subclinical atherosclerotic disease (SAD). The Mediterranean diet (MDiet) is known for its cardiovascular benefits, but the combined influence of both MDiet adherence and physical activity (PA) on SAD progression has not been previously documented. Objective: We aimed to investigate how adherence to a healthy lifestyle, defined as MDiet adherence and PA level, influences SAD progression in subjects from the ILERVAS cohort follow-up. Methods: A study on 3097 participants from the ILERVAS prospective cohort was conducted. MDiet adherence was assessed using the MEDAS score, and PA categories were established using the IPAQ, both categorized into low, moderate, and high levels. Two different lifestyle scores integrating the MDiet and PA categories were built. The presence of atherosclerotic plaques was assessed by carotid and femoral ultrasound examination. Demographic, clinical, and biochemical data were also obtained. Multivariable linear, logistic, and Poisson regression models adjusted for potential confounders were used to analyze the association between the lifestyle scores and SAD progression, as well as the MDiet and PA as separate variables and number of territories with plaque. Results: A healthier lifestyle score did not show an effect on SAD progression. However, a higher MEDAS score was associated with a 3% decrease in the number of territories with plaque (IRR 0.97, 95% CI 0.96–0.99, p < 0.001), suggesting a protective effect of the adherence to the MDiet. PA did not show a significant association (IRR 1.00, 95% CI 1.00–1.00, p = 0.269). Older age, hypertension, dyslipidemia, smoking, and lower eGFR were associated with SAD progression, while the female sex was protective (IRR 0.67, 95% CI 0.63–0.72, p < 0.001). Conclusions: The findings of this study show that higher adherence to the MDiet is associated with reduced incidence of SAD, indicating its potential role in cardiovascular prevention strategies. Although a higher lifestyle score or physical activity levels did not show any significant effect, promoting the MDiet, alongside managing traditional cardiovascular risk factors, could be an effective public health intervention to prevent atherosclerosis and reduce the burden of cardiovascular disease.