It is estimated that around 25% of the population worldwide experience adverse reactions to food, which are very diverse based on both etiology and clinical presentation. According to the pathophysiological processes involved, adverse reactions to foods can be broadly classified as sensitivities or intolerances, depending on whether they are immune-mediated, or not. Specifically, food sensitivities have become a growing clinical, economic, and social problem nowadays. Although the reason for the increased prevalence of well-determined food sensitives such as celiac disease and food allergies is not well understood, the role of microbes in both inducing and protecting from these conditions has been proposed. First, several studies suggest that the gut microbiota, the vast number of microbes that live in our digestive tract, influence the appearance of different adverse reactions to food. These studies are based on observational changes in the composition and function of the fecal microbiota of celiac, allergic and food intolerant patients when compared to controls or healthy participants. Second, infectious microbial agents have been related to the loss of oral tolerance towards dietary components and the occurrence of different adverse reactions to foods. However, how could microbes participate in food sensitivities and intolerances from a mechanistic point of view? Preclinical studies with animal models not only support observations in humans, they also show a causal role of microbes in the occurrence and course of these diseases, while informing the specific underlying mechanisms. The aim of this review is to summarize the scientific evidence that supports the role of microbes in the main adverse reactions to food described, with an emphasis on the underlying mechanisms. The discovery of the main molecular pathways involved in pathogenic reactions to diet foods will accelerate the development of new therapeutic approaches with the aim of preventing and treating food sensitivities and intolerances.