Animal and plant microbiomes are of strategic importance to improve food productivity and quality, thanks to their positive action on host physiology, energy homeostasis and feed efficiency. On the other hand, environmental microbiomes can be crucial to achieving sustainable intensification of food systems, by enhancing the ecosystem capacity to buffer food system pressures on the environment. Finally, by definition, microbiomes are central in contrasting the biodiversity crash, ensuring a large panel of functional diversity and functional redundancy strategic for the resilience of the ecosystem.