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Coffee contains more than one thousand volatile compounds, of which approximately thirty play a key role in the perception of beverage sensory attributes and are considered major determinants of cup quality. The precursors of these compounds are formed during coffee cultivation and postharvest processing and are subsequently transformed during roasting through multiple chemical reactions. Among the most relevant classes of volatile compounds are furans, pyrazines, organic acids, alcohols, and aldehydes. The composition and relative abundance of these compounds enable discrimination between high-quality coffees and those presenting sensory defects. This study evaluated 48 volatile compounds in coffee beans obtained from fruits harvested at three ripening stages and subjected to fruit reserve and prolonged mucilage fermentation. Fruit reserve significantly modified the concentrations of compounds such as ethyl acetate, acetic acid, and ethanol, contributing to the development of fruity and red-fruit sensory notes, particularly after 48 h of reserve. In contrast, prolonged mucilage fermentation of fruits at advanced ripening stages and under higher fermentation temperatures reduced the scores of five sensory attributes and promoted fermenting flavor defect which is commonly associated with increased concentrations of volatile compounds such as hexanal and 3-methylbutanoic acid.