Fermentation and clone selection modulate the biochemical and nutritional profile of cocoa beans grown in the southwestern Amazon

The interaction between cocoa clones and post-harvest practices, such as fermentation and non-fermentation of beans, influences cocoa quality in the Amazon. However, these effects remain poorly understood. This study evaluated the effects of fermentation and non-fermentation on the biochemical and nutritional attributes of beans from different clones and on plant productivity in the southwestern Brazilian Amazon. Nine cocoa clones cultivated in Rondônia were analyzed under two post-harvest conditions (fermented and non-fermented). The following parameters were assessed: N, P, K, S, Ca, Mg, B, Cu, Fe, Mn, Zn, total phenolic compounds, tannins, anthocyanins, and the metabolites proline, glycine betaine (GB), malondialdehyde (MDA), and superoxide dismutase (SOD) activity. In general, fermented beans showed higher levels of amino acids, SOD, K, Mg, GB, Zn, and Fe, while non-fermented beans exhibited higher contents of sugars, phenolic compounds, tannins, proteins, MDA, and anthocyanins. Clone CCN 51 showed a balanced biochemical profile under both post-harvest conditions, while EEOP 63 combined high productivity with strong functional performance. These findings suggest that selecting appropriate clones for fermented and non-fermented systems can improve cocoa bean quality in the Amazon, aligning productivity, health-related traits, and innovation in the fine chocolate market.