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Plants do not grow in isolation; they interact with diverse microorganisms in their habitat.The development of techniques to identify and quantify the microbial diversity associated with plantscontributes to our understanding of the complexity of environmental influences to which plants areexposed. Identifying interactions which are beneficial to plants can enable us to promote healthygrowth with the minimal application of agrochemicals. Beneficial plant–microbial interactionsassist plants in acquiring inaccessible nutrients to promote plant growth and help them to copewith various stresses and pathogens. An increased knowledge of plant–microbial diversity can beapplied to meet the growing demand for biofertilizers for use in organic agriculture. This reviewhighlights the beneficial effects of soil–microbiota and biofertilizers on improving plant health andcrop yields. We propose that a multi–omics approach is appropriate to evaluate viability in thecontext of sustainable agriculture.