Up to the last update, the gut microbiome (GM) had been associated with a different physiologic host process, including those affecting cardiovascular health. The carotid intima-media thickness (IMT) is an indicator of atherosclerosis and cardiovascular risk. The GM influence on atherosclerosis progression has garnered growing attention in recent years but the consensus in subclinical atherosclerosis remains elusive. The aim of this narrative review is to investigate the connection between the GM and carotid IMT, encompassing mechanisms like the microbiome impact on metabolite production, and systemic inflammation, and its effects on endothelial function. The literature analysis revealed that the GM appears to exert an influence on carotid IMT development, likely through mechanisms involving metabolites’ production, systemic inflammation, and endothelial function modulation. Additional research, however, is needed to finely elucidate the relationship between the GM and atherosclerosis. Specifically, more extensive studies are required to pinpoint individuals at the highest risk of developing atherosclerosis based on their GM composition. This will facilitate the enhancement and optimization of cardiovascular disease prevention strategies and enable the treatments’ customization for each patient. Further investigations are required to refine patient outcomes in the context of probiotics and other interventions aimed at improving microbiome composition and function.