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[Display omitted] • Organic acid concentration influenced volatile organic compounds formation. • Sensory analysis revealed high-quality chocolate profiles. • High organic acid concentrations yielded fruity and acidic chocolates. • Low acid concentrations resulted in nutty and cocoa-rich flavors. • Metabolomic analysis highlighted the impact of organic acid concentration. Fine-flavored chocolates are distinguished by their complex and distinct flavor profiles, which includes notes such as floral, fruity, nutty, and spicy. This study sought to modulate the flavor development of chocolates by establishing controlled processing conditions during the transformation from seed to bean in a laboratory setting, to produce superior quality chocolates. Our experimental setup comprised two varying temperature levels (30 °C and 45 °C) and three organic acids (OAs: acetic, lactic, and citric acids) at concentrations of 1–30 g/L to adjust the pH of the transformation system. Our study focused on how these conditions affect the development of distinct flavor profiles in chocolate bars, emphasizing the enhancement of fine-flavor notes. Flavor development was monitored through the untargeted metabolomics of cocoa beans and analyzing the volatile compounds and sensory profiles of the resultant chocolates. This study revealed that OA concentration markedly influenced metabolite formation, particularly affecting peptides, volatile organic compounds, and flavor notes. Chocolates derived from seeds processed with 30 g/L acid solutions demonstrated enhanced fruitiness and acidity, whereas those processed with 1 g/L acid solutions exhibited pronounced nuttiness and cocoa taste attributes but lower acidity. These findings underscore the significance of meticulously managing flavor development processes to produce fine-flavored chocolates with unique aromatic profiles. Crucially, variables in the controlling process, such as temperature and pH, are essential for fine-tuning flavor attributes, enabling the correlation and identification of key quality biomarkers to elucidate flavor development pathways. [ABSTRACT FROM AUTHOR]