All multicellular organisms, be they heterotroph or autotroph, saprophyte or detritivore, herbivore or carnivore, harbour a distinct microbiome that is adapted to aid the flow of nutrients to its host. Often these symbioses have a long evolutionary history. This microbially mediated release of nutrients has implications for host health at the organismal scale, as well as environmental turnover and regulation of nutrient cycles on the global scale. Classic examples of plant–soil nutrient dynamics include symbiotic nitrogen fixation by rhizobia and Frankia spp. in leguminous and non-leguminous species, respectively, and the mycorrhizal symbioses that facilitate the release of phosphorous for plants by fungi in return for carbon produced via photosynthesis. A number of invertebrate–microbe symbioses have also been studied in detail, including aphids and nutrient-fixing symbionts, fungal gardens of leafcutter ants and termites, and honeybees and pollen digestion. We provide an overview of these here, in addition to the interactions between gut microbes and nutrition in vertebrates, particularly humans and agriculturally important species.