Allergic reactions leading to food allergies, asthma or atopic eczema symptoms, are significantly impacted by the gut microbiome. Dysbiosis, an imbalance in gut microbiota, can increase the risk of these conditions. Food allergies are caused by dysregulation in IgE synthesis, but commensal bacteria in the human microbiota can regulate the immune response and prevent the development of food allergies. Exposure to microbes during infancy can positively influence allergy development. Treatment options include food allergy immunotherapy, pharmacological treatments, prebiotics and probiotics. Studies show that the gut microbiota composition differs in individuals with allergic and non-allergic asthma compared to healthy individuals, with higher richness but lower diversity of gut microbiome in asthmatic individuals. The relationship between the intestinal microbiota and the occurrence of atopic eczema is clear, with differences in the number of types of bacteria contributing to the activation of the immune system and the appearance of atopic eczema. Understanding the complex interactions between the gut microbiome and the immune system may lead to new therapeutic strategies for the prevention and treatment of allergic diseases, which have a significant impact on patients’ lives.