Fermented foods represent a significant fraction of human diets. Although their impact on health is positively perceived, an objective evaluation is still missing. We have, therefore, reviewed meta-analyses of randomized controlled trials (RCT) investigating the relationship between fermented foods and non-transmissible chronic diseases. Overall, after summarizing 25 prospective studies on dairy products, the association of fermented dairy with cancer was found to be neutral, whereas it was weakly beneficial, though inconsistent, for specific aspects of cardio-metabolic health, in particular stroke and cheese intake. The strongest evidence for a beneficial effect was for yoghurt on risk factors of type 2 diabetes. Although mechanisms explaining this association have not been validated, an increased bioavailability of insulinotropic amino acids and peptides as well as the bacterial biosynthesis of vitamins, in particular vitamin K2, might contribute to this beneficial effect. However, the heterogeneity in the design of the studies and the investigated foods impedes a definitive assessment of these associations. The literature on fermented plants is characterized by a wealth of in vitro data, whose positive results are not corroborated in humans due to the absence of RCTs. Finally, none of the RCTs were specifically designed to address the impact of food fermentation on health. This question should be addressed in future human studies.