A growing body of evidence suggests that the establishment of a balanced gut microbiome is crucial for many aspects of human health. This is because gut microbes are involved in key processes such as host metabolism and immune system regulation and therefore help to maintain homeostasis in the human body. The gut microbiome and the immune system evolve in parallel, and their interactions are established during infancy and early childhood. Altered gut colonization patterns and reduced gut diversity during early life have been associated with the development of several diseases, including allergies, later in life. Undoubtedly, nutrition is a key regulator of the gut microbiome and plays a vital role in the development of such diseases. In this chapter, we will discuss how the gut microbiome interacts with the immune system in order to achieve immune tolerance. We will also describe the factors that influence the gut colonization process during early life and how disruption of this process can lead to the development of allergic diseases. Finally, we will focus on the role of nutrition during pregnancy, infancy, and early childhood in the development of the immune system. In particular, we will focus on the role of certain nutrients and food components, such as human milk oligosaccharides (HMOs), short-chain fatty acids (SCFAs), and omega-3 polyunsaturated fatty acids (PUFAs).