Insects host microbes and interact with them throughout their life cycle. This microbiota is an important, if not essential, partner participating in many aspects of insect physiology. Recent omics studies have contributed to considerable advances in the current understanding of the molecular implications of microbiota during insect development. In this review, we present an overview of the current knowledge about the mechanisms underlying interactions between developing insects and their microbial companions. The microbiota is implicated in nutrition, both via compensating for metabolic pathways lacking in the host and via regulating host metabolism. Furthermore, the microbiota plays a protective role, enhancing the insect's tolerance to, or resistance against, various environmental stresses.