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Mycorrhizal inoculation improves nutrient uptake in a range of host plants. Insufficient nutrient uptake by plants grown hydroponically is of major environmental and economic concern. Tomato seedlings, therefore, were treated with a mycorrhizal inoculant (Mycoroot™) at transplanting to potentially enhance nutrient uptake by the plant. Then seedlings were transferred to either a temperature-controlled (TC) or a non-temperature-controlled (NTC) tunnel and maintained using the recommended (100%) or a reduced (75% and 50%) nutrient concentration. Plants grown in the NTC tunnel had significantly poorer plant growth, lower fruit mineral concentration, and lower yield compared with fruit from plants in the TC tunnel. Leaves from plants in the NTC tunnel had higher microelement concentrations than those in the TC tunnel. Highest yields were obtained from plants fertigated with 75% of the recommended nutrient concentration, and not from the 100% nutrient concentration. Application of arbuscular mycorrhizal fungi (AMF) neither enhanced plant growth, nor yield, nor fruit mineral nutrient concentrations. However, temperature control positively affected the fruit Mn and Zn concentration in the TC tunnel following AMF application.