Molybdenum (Mo) is a crucial microelement for both, humans and plants. The use of agronomic biofortification techniques can be an alternative method to enhance Mo content in vegetables. Concomitantly, arbuscular mycorrhizal fungi (AMF) application is a valuable strategy to enhance plant performances and overcome plant abiotic distresses such as microelement overdose. The aim of this research was to estimate the direct and/or indirect effects of Mo supply at four doses [0.0, 0.5 (standard dose), 2.0 or 4.0 μmol L−1], alone or combined with AMF inoculation, on plant performances. In particular, plant height and first flower truss emission, productive features (total yield, marketable yield and average marketable fruit weight) and fruit qualitative characteristics (fruit dry matter, soluble solids content, titratable acidity, ascorbic acid, lycopene, polyphenol, nitrogen, copper, iron and molybdenum) of an established cherry tomato genotype cultivated in soilless conditions were investigated. Moreover, proline and malondialdehyde concentrations, as well as Mo hazard quotient (HQ) in response to experimental treatments were determined. A split-plot randomized experimental block design with Mo dosages as plots and +AMF or -AMF as sub-plots was adopted. Data revealed that AMF inoculation enhanced marketable yield (+50.0 %), as well as some qualitative traits, such as fruit soluble solids content (SSC) (+9.9 %), ascorbic acid (+7.3 %), polyphenols (+2.3 %), and lycopene (+2.5 %). Molybdenum application significantly increased SSC, polyphenols, fruit Mo concentration (+29.0 % and +100.0 % in plants biofortified with 2.0 and 4.0 μmol Mo L−1 compared to those fertigated with the standard dose, respectively) and proline, whereas it decreased N (−25.0 % and −41.6 % in plants biofortified with 2.0 and 4.0 μmol Mo L−1 compared to those fertigated with the standard dose, respectively). Interestingly, the application of AMF mitigated the detrimental effect of high Mo dosages (2.0 or 4.0 μmol L−1). A pronounced advance in terms of plant height 45 DAT, fruit lycopene concentration and fruit Fe, Cu and Mo concentrations was observed when AMF treatment and Mo dosages (2.0 or 4.0 μmol Mo L−1) were combined. Plants inoculated or not with AMF showed an improvement in the hazard quotient (HQ) in reaction to Mo application. However, the HQ - for a consumption of 200 g day−1 of biofortified cherry tomato - remained within the safety level for human consumption. This study suggests that Mo-implementation (at 2.0 or 4.0 μmol L−1) combined with AMF inoculation could represent a viable cultivation protocol to enhance yield, produce premium quality tomato fruits and, concomitantly, improve Mo dose in human diet. In the light of our findings, further studies on the interaction between AMF and microelements in other vegetable crops are recommended.