The worrying number of children suffering from undernutrition and consequent stunting worldwide makes the understanding of the relationship between nutritional status and postnatal growth crucial. Moreover, it is now well established that undernourished children harbor an altered microbiota, correlating with impaired growth. In this review, we describe how murine models have been used to explore the functional relationships between endocrine regulation of growth, nutrition and gut microbiota. In numerous Mammalian species, postnatal growth is mainly regulated by the conserved GH/IGF1 somatotropic axis that acts through endocrine and paracrine pathways, notably enabling longitudinal bone growth. Recent studies have demonstrated that the microbiota effects on growth could involve a modulation of GH and IGF1 circulating levels. Besides, the GH/IGF1 somatotropic axis may regulate the gut microbiota composition and diversity. Studying the bidirectional relationship between growth hormones and the gut microbiome could therefore help developing microbiota-targeting therapies in order to reduce the long-term consequences of stunting.