The tomato is a key fruit in China. However, the drive to produce higher-quality tomatoes has resulted in fertilizer overuse, soil degradation, and environmental pollution in recent years. Therefore, investigating the effects of balanced fertilization on the nutritional and flavor qualities of tomato plants is crucial. This study applied four fertilizer treatments to assess their effects on sugar and acid contents, sugar-metabolism-related enzyme activity, nitrate levels, ascorbic acid, pigments, polyphenols, and volatiles, and we performed a correlation analysis. The results showed that balanced fertilization increased glucose and fructose contents by 45% and 31% compared to CK (conventional fertilizer), while tartaric, citric, acetic, malic, and shikimic acid contents were reduced by 59%, 27%, 22%, 26%, and 4%, respectively. Additionally, balanced fertilization increased the activities of sucrose synthase (SS), sucrose phosphate synthase (SPS), acid invertase (AI), and neutral invertase (NI) by 58%, 26%, 19%, and 35%, respectively, compared to CK (conventional fertilizer) and upregulated the expression of phosphoenolpyruvate carboxykinase (PEPCK), neutral invertase (NI), sucrose-phosphate synthase (SPS), and fructose-1,6-bisphosphatase (FBP) genes. Moreover, balanced fertilization significantly enhanced the polyphenol content, as well as the diversity and concentration of volatiles. Correlation analysis confirmed that sugar-metabolism-related enzymes and genes were positively correlated with sugar fractions and negatively correlated with the organic acid content. Principal components analysis demonstrated that the balanced fertilization treatment was distinct from the other treatments, and all polyphenols, except for caffeic acid, were positively associated with balanced fertilization.
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