When it comes to the agroecological transition, biodiversity plays a central role in terms of the ecosystem services provided and their role in helping crops adapt to abiotic and biotic stresses. Ecological processes that can support crop adaptation to stresses include biological interactions, such as those between microorganisms and pests (e.g. competition, predation and parasitism), and interactions between microorganisms, plants and pests that modulate plant immunity. The impact of microbiota on crop health and yield has been demonstrated in recent studies describing the relationships between microbiota diversity and various plant phenotypic traits (e.g. disease suppression or resistance and growth promotion). The farming system, plant genotype and plant association are all factors that influence the composition of the plant microbiota, and they must be considered to develop crop management strategies based on improving or maintaining beneficial plant-microbiota interactions. Managing microbiota to improve agricultural production can be achieved by leveraging different plant associations to modulate the soil microbiota and/or by inoculating crops with a microbial strain or consortium with properties that are beneficial to plant growth and health.