Dietary changes have accompanied the evolution of humanity and is proven to be fundamental in human evolution and well-being. Nutrition is essential for survival and as a matter of health and equilibrium of the human body. About 1/3 of the human diet is composed by fermented foods and beverages, which are widely distributed and consumed in different societies around the world, no matter the culture and lifestyle. Fermented foods are derived from the fermentation process of different substrates by microorganisms, and more importantly to humans, by those with beneficial characteristics, due to the positive impact on health. Food is transformed in the gut, gaining new proprieties, and increasing its value to the organism. The effects of fermented foods and beverages can be assessed by its influence at the gut microbiota level. Recent studies show the major importance of the gut microbiota role in modulating the organism homeostasis and homeorhesis. More crosslinks between health, gut microbiota and diet are being established especially in the gut–brain axis field. Therefore, the benefits of diet, in particularly of fermented foods and beverages, should be studied and pursued in order to promote a good health status.