In this study, we have analysed the Amazonian variety EETP801 Cacao, grown under sustainable organic conditions, in comparison to CCN51 cacao grown on a neighbouring commercial farm using standard practices and an European commercial cacao powdered beverage. The overall metabolite profile was analysed by high performance TLC analyses (HPTLC), the volatile fraction by head-space gas chromatography–mass spectrometry (HS-GC-MS) and the xanthine alkaloids by quantitative liquid chromatography-UV photodiode array (HPLC-DAD) analyses. Total polyphenol content was determined by the Folin-Ciocalteu method. Despite the reduced production of cocoa by the EETP801 cultivar in comparison with the CCN51 cultivar, the obtained produce is significantly richer in theobromine (130 mg vs 170 mg per g of cacao) with CCN51 having double concentration of theophylline (12.6 vs 6.5 mg per g of cacao). Qualitatively, EETP-801 has the same polyphenolic composition (as per the HPTLC fingerprint) of the CCN51 cultivar but shows more traces of glycosylated flavonoids (rutin). The HS-GC-MS analyses revealed that the fragrance of both Amazonian cacao samples was superior to that of the commercial sample. The variability in the artisan fermentation and roasting processes influenced certain aspects of the volatile composition. The cultivar EETP801 is a viable option for a more ecologically conscious sector of the cocoa beverages consumer group.