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NaCl stress can enhance the accumulation of phenolic compounds in soybean during germination. In the present study, effects of gamma-aminobutyric acid (GABA) and Ca²⁺ on the biosynthesis of phenolic compounds in soybean sprouts germinated with NaCl stress were investigated. Results showed that addition of Ca²⁺ increased the content of total phenolics, phenolic acids, and isoflavonoids in soybean sprouts by ca. 15%, 7%, and 48%, respectively, through enhancing the activities of three key enzymes involved in the biosynthesis. On the other hand, addition of LaCl₃, a calcium channel blocker, inhibited the synthesis of phenolic compounds, indicating that Ca²⁺ plays an important role in the synthesis of these compounds in soybean sprouts. Addition of GABA can increase the content of Ca²⁺ in soybean sprouts by ca. 20% and alleviate the inhibition of LaCl₃ on phenolics biosynthesis in soybean sprouts. Similarly, addition of Ca²⁺ can reverse the inhibition of 3-mercaptopropionate, an inhibitor of endogenous GABA synthesis, on the biosynthesis of phenolic compounds in soybean sprouts under NaCl stress. To conclude, both GABA and Ca²⁺ can enhance the biosynthesis of phenolic compounds in soybean sprouts and there was an interaction between their effects on the promotion of phenolic compounds biosynthesis.