The Mediterranean diet (MD) is widely recognized for its health benefits, particularly in modulating gut microbiota composition and reducing the risk of metabolic, cardiovascular, and neurodegenerative diseases. Characterized by a high intake of plant-based foods, monounsaturated fats, and polyphenols, primarily from extra virgin olive oil, the MD fosters the growth of beneficial gut bacteria such as , , and , which produce short-chain fatty acids that enhance gut barrier integrity, reduce inflammation, and improve metabolic homeostasis. Clinical and preclinical studies have proved that the MD is associated with increased microbial diversity, reduced pro-inflammatory bacteria, and improved markers of insulin sensitivity, lipid metabolism, and cognitive function. Additionally, the MD positively influences the gut microbiota in various conditions, including obesity, cardiovascular disease, and neurodegeneration, potentially mitigating systemic inflammation and enhancing neuroprotective mechanisms. Emerging evidence suggests that MD variants, such as the Green-MD, and their integration with probiotics can further optimize gut microbiota composition and metabolic parameters. While the beneficial impact of the MD on the gut microbiota and overall health is well supported, further long-term clinical trials are needed to better understand individual variability and improve dietary interventions tailored to different populations.