In most fleshy fruit, malate and citrate represent the predominant organic acids, serving as key determinants of flavor and nutritional quality. Their concentrations undergo dynamic changes driven by complex biosynthetic pathways and multilayered genetic regulation. Beyond their impact on taste, these organic acids have pleiotropic effects, influencing secondary metabolism and postharvest performance. This review synthesizes current knowledge on the molecular mechanism governing malate and citrate metabolism, including genes responsible for biosynthesis, catabolism, and transport, as well as regulatory networks orchestrated by transcription factors, environmental factors, and phytohormones such as ethylene, abscisic acid (ABA), auxin, gibberellin (GA), and salicylic acid (SA) during fruit development and ripening. We also explored how the dynamics of citrate and malate interact with critical quality attributes, including starch metabolism, textural properties, and postharvest performance, while highlighting domestication-selected genes that influence acidity. Finally, we propose an integrative model delineates the multifactorial regulation of organic acid metabolism in fleshy fruits.

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