Increased prevalence of food allergies in the last thirty years has been attributed to lifestyle changes in Westernized countries. Among the environmental factors, nutritional factors and their interaction with the gut microbiome in early life are thought to have an important role in the observed epidemiological change. The gut microbiome synthesizes bacterial metabolites, which represent a link among gut microbiome, nutrition, and immune system. The main metabolites produced by gut microbiome are short-chain fatty acids (SCFAs). SCFAs have multiple beneficial effects on human health including protective effects in autoimmune and inflammatory diseases. Among SCFAs, butyrate is essential for maintaining gut immune homeostasis and exerts a pivotal role in immune tolerance with strong anti-inflammatory effects in allergic diseases. Recent findings suggest that butyrate takes part in the development of immunological tolerance to food, especially in the first 1000 days of life. Herein, we provide a critical review of the scientific literature on the role of butyrate for prevention and treatment of food allergies with focus on the complex interplay among early life nutrition, gut microbiome, and immune system.