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This study attempted to improve commercial Arabica coffee quality by integrating flavor precursors with anaerobic germination. Using raw coffee beans as materials, anaerobic germination was conducted with 5 g/100 g of flavor precursors (sucrose, glucose, fructose). The chemical composition and sensory quality of roasted coffee beans were analyzed. Results showed that adding flavor precursors facilitated the harmonization of water-soluble chemical components and altered aroma characteristics. Specifically, the inclusion of flavor precursors significantly increased the levels of 5-Hydroxymethylfurfural and volatile aldehydes. Principal component analysis (PCA) on chemical composition dataset revealed 48.7% variability. Sensory analysis, employing the Specialty Coffee Association (SCA) cupping protocol, demonstrated that combining flavor precursors with anaerobic germination transformed coffee flavor properties, enhanced quality, and substantially increased sensory scores (p < 0.05). Sucrose supplementation produced the highest sensory score and intensified fruity flavor attributes. Therefore, adding different flavor precursors forms distinct flavor characteristics, conducive to further improving the quality of germinated coffee.