The connection between diet and cognitive function occurs since intrauterine life. Nutrition also impacts the immune system, as priming of the adaptive immune response towards an antigen may depend on metabolic factors. The key aspect is represented by the presence of microbiota-gut-brain axis. The bidirectional communication between the microbial community dwelling in the gut (gut microbiota) and the brain occurs through various pathways including the vagus nerve, the immune system, neuroendocrine pathways and bacterial derived metabolites. The gut microbiota exerts numerous functions for gut homeostasis and host health, such as metabolism of undigested nutrients, supply of beneficial microbial metabolites, defense against enteric pathogens and maturation of the immune system. Nutrients and microbial products pass through the intestinal epithelial barrier where they participate in enterocytes’ physiology and drive the behaviour of immune cells. The microbiota-gut-brain axis is involved in neurodegeneration, by affecting, thus, several aspects of health regarding energy metabolism, immune system and neuronal function. Numerous factors have been highlighted to influence gut microbiota composition, including diet composition and nutritional status that are modifiable factors. Optimal nutritional status and healthy gut microbiota are crucial for maintaining brain health. Unbalanced dietary patterns may affect the microbial community and, as a consequence, may affect brain physiology and its predisposition to neurodegenerative diseases.