## 4 Conclusions  
Our study has allowed us to characterize stages according to the time of spontaneous and starter culture fermentation in cocoa. In SF, the first stage (0 to 24 h) was characterized by a higher content of methylxanthines and flavan-3-ols and a high level of TPC, AC, and AA; subsequently, the second stage was characterized by a high concentration of antioxidant profile variables, but it was lower than in the first stage; finally, in the third stage, the antioxidant profile variables studied were lower than in the first two stages. In the case of SC, the first stage (0 to 48 h) was characterized by higher values of AA, TPC, methylxanthines, and epicatechin; the second stage (72 h to 96 h) was characterized by low values of the antioxidant profile and a more significant variation of fermentation times; finally, the last hours of fermentation (stage 3) were characterized by similar concentrations of caffeine and catechin to the first and second stages. The study allowed monitoring the concentration of volatile compounds in cocoa beans, highlighting that the leading families reported were acids, alcohols, aldehydes, ketones, esters, hydrocarbons, and furans. In both fermentations, a high concentration of the main aromatic VCs (e.g., acetoin, ethanol, 2-heptanol, 2-pentanol, acetic acid, 3-methyl-1-butanol, among others) can be observed between 48 and 96 h for the cocoa bean. It was also found that there is a higher concentration of alcohols and esters when a starter culture (_S. cerevisiae_) is used, which was possibly because the yeast facilitates the release of compounds. Finally, the study has shown that prolonged fermentation times decrease the antioxidant potential and affect the presence of VCs precursors of aroma and final flavor in cocoa, demonstrating the need to reduce the fermentation time in native Amazonian cocoa. **Supplementary Materials:** The following supporting information can be downloaded at: [[https://www.mdpicom/article/10.3390/foods12173291/s1](https://www.mdpicom/article/10.3390/foods12173291/s1)]([https://www.mdpicom/article/10.3390/foods12173291/s1](https://www.mdpicom/article/10.3390/foods12173291/s1)), Figure S1. Chromatogram of caffeine standard at 300 ppm; Figure S2. Chromatogram of theobromine standard at 300 ppm; Figure S3. Chromatogram of catechin standard at 300 ppm; Figure S4. Chromatogram of epicatechin standard at 300 ppm; Table S1: Average values of pH, dissolved oxygen and temperature (\({}^{\circ}\)C) in cocoa pulp-bean mass in SF and SC; Table S2: Average values of physicochemical parameters of cocoa beans during fermentation (SF and SC); Table S3: Concentration of main volatile compounds (\(\mu\)g/g) by GC-MS in cocoa beans during spontaneous fermentation; Table S4: Concentration of main volatile compounds (\(\mu\)g/g) by GC-MS in cocoa beans during fermentation with starter culture. **Author Contributions:** Conceptualization, E.M.C.-A. and C.R.B.-Z. ; methodology, N.R.-H., A.J.P.-M., D.F.T.-R. and A.F.I.-C.; software, I.Y. and I.M.M.M.M. ; validation, I.Y, I.S.C.-C. and E.M.C.-A. ; formal analysis, A.J.P.-M. and D.F.T.-R.; investigation, E.M.C.-A., J.L.M.-Q. and C.R.B.-Z. ; resources, E.M.C.-A. and I.Y. ; data curation, A.J.P.-M. and C.R.B.-Z. ; writing--original draft preparation, C.R.B.-Z. and E.F.-R.; writing--review and editing, I.S.C.-C. and E.M.C.-A. ; visualization, C.R.B.-Z. and E.M.C.-A. ; supervision, I.S.C.-C. and G.C.A.C.-J. ; project administration, L.D.M.-A. All authors have read and agreed to the published version of the manuscript. **Funding:** This research was funded by the Consejo Nacional de Ciencia, Tecnologia e Innovacion Tecnologica-Concytec (project: Estudio metabolomico del proceso de fermentacion de cacao (_Theo-brona acao_ L) native organico fino de aroma, contract No. 56-2021-FONDECYT; and Project: Cristalizacion y polimorfismo de la manteca de cacao en granos de diferentes origenes geograficos y su impacto en la calidad de chocolates finos, contract No. PE501077920-2022) of the Peruvian Government, The World Bank Group.