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Synergistic studies of microorganisms in the last decade have been mostly directed towards their biofertilizing effects on growth and crop yield. Our research examines the role of a microbial consortium (MC) on physiological responses of Allium cepa hybrid F1 2000 under water and nutritional deficit in a semi-arid environment. An onion crop was established with normal irrigation (NIr) (100% ETc) and water deficit (WD) (67% ETc) and different fertilization treatments (MC with 0%, 50% and 100% NPK). Gas exchange (Stomatal conductance (Gs), transpiration (E) and CO 2 assimilation rates (A)) and leaf water status were evaluated throughout its growth cycle. The MC + 50% NPK treatment with NIr maintained similar A rates to the production control. A. cepa decreased Gs by approximately 50% in the WD treatment. The highest water use efficiency (WUE) and an increase in the modulus of elasticity in response to water stress were obtained for the 100% NPK treatment under non-inoculated WD. The onion hybrid F1 2000 was tolerant to water stress and under non-limiting nutrient conditions, irrigation may be reduced. The MC facilitated the availability of nutrients under NIr allowing a 50% reduction in the application of high doses of fertilization without affecting yield, resulting in a suitable agroecological strategy for this crop., (© 2023. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.)