Fermentation is a critical postharvest stage influencing cocoa quality through changes in volatile and bioactive compounds. This study evaluated these dynamics in Criollo cocoa beans from Amazonas, Peru, during spontaneous fermentation (SF), Saccharomyces cerevisiae -inoculated fermentation (SC), and drying. Temperature increased faster in SC than SF, while both treatments reached pH conditions associated with aroma precursor formation. Alcohols had the highest relative abundance among volatile families, whereas esters comprised the largest number of tentatively identified compounds; 2,3-butanediol, 2-heptanol, and 2-phenylethanol were the most abundant volatiles. SC yielded more tentatively identified volatiles at the end of fermentation. Drying increased the relative abundance of pyrazines and ketones, reorganizing the volatile profile during moisture loss. Processing stage and fermentation time were the main factors associated with differences in volatile composition. Theobromine remained the predominant bioactive compound, while SC retained higher catechin and epicatechin concentrations than SF at the end of fermentation.