Plant roots associate with diverse communities of arbuscular mycorrhizal fungi (AMF), providing the plant with mineral nutrients in exchange for carbohydrates. We investigated how onion genotype and fungal species interact to determine the benefit of the symbiosis to the plant and the potential benefit of a mixed AMF community. Ten onion genotypes were inoculated with five different AMF species, or a mixture of all five, then plant growth/nutrient uptake was compared to non-inoculated controls. 18S ribosomal RNA (rRNA) terminal restriction fragment length polymorphism was used to compare the abundance of each AMF species between genotypes. Growth and nutrient uptake were significantly different between genotypes and AMF species, but no genotype×AMF interaction was observed, indicating a general response to AMF. Potentially useful pre-breeding material was identified for use in low-input systems. Inoculation of plants with AMF led to significant increases in the concentrations of N, P and Cu, whereas significant decreases in Ca, K, Na, Fe, Mn and Zn were observed. There were significant differences between AMF species in their effect on plant nutrition. Inoculation with Acaulospora spinosa led to a significant increase in shoot S concentration which may have implications for plant defence and pungency. No additive effect of a mixed community was observed. Contrasting genotypes showed subtly different preferences for associating with AMF from a mixed community, suggesting a selection process controlled by the plant and/or the fungi. The implications of this work for the development of sustainable, low-input systems are discussed.