Background&#xa0;and scope <p>Magnesium (Mg) deficiency occurs commonly in acidic soils and intensive crop production systems. How preharvest Mg limitation affects fruit postharvest quality remains, to date, elusive at physiological- and molecular-levels.</p> Methods and results <p>Using turface-cultured tomatoes (<i>Solanum lycopersicum</i>), we investigated the multiple morphological characteristics of tomato fruit to Mg deficiency during three late growth stages by employing physiological and molecular approaches. Results showed that total Mg²⁺ concentration was decreased by up to 14.5–27.0% under Mg limitation (0.02&#xa0;mM MgSO₄.7H₂O), and the concentration of competing cations (i.e., K⁺, Ca²⁺, and Na⁺) was increased in tomato fruits. The reduced biosynthesis and accumulation of carbohydrates (i.e., soluble sugars and starch) and carotenoids decreased the harvestable yield and impaired eleven important fruit postharvest characteristics (i.e., height, width, perimeter, pericarp, and color indexes). Hormonal imbalance (i.e., IAA, ABA, GA3, and ZR) likely delayed the fruit ripening process. Transcriptome profiling indicated the alteration of major biological processes and 119, 279, and 180 genes were differentially expressed at the green mature, breaker, and red mature stages, respectively. Consistent with transcriptomic, three sugar/sucrose transportation-related genes were differentially expressed in fruit tissues. Notably, the low accumulation of total free amino acids (30.5–62.3%) and soluble proteins (25.0–22.7%) in the fruit aligned with the differential expression of eight genes involved in amino acid transport/metabolism.</p> Conclusion <p>These findings deepen our understanding of the essential role of Mg in providing carbohydrates and amino acids during fruit ripening and pave the way for genetic improvement to obtain high-quality fleshy fruit under Mg-deficient conditions.</p>