The phenotypic characterization of cacao (Theobroma cacao L.) plays an important role in the generation of information for the conservation of cacao germplasm. The objective of this study is to characterize phenotypically 146 ecotypes of fine-aroma native cacao (FFNC) from northeastern Peru that were collected from 280 to 1265 metres above sea level. Morphological descriptors of fruits and seeds, sensory characteristics, and productivity descriptors were used. The data obtained were analyzed using descriptive statistics with pie charts, distribution histograms, and multiple correspondence analysis. The results showed that 76.7% of the cocoa ecotypes had green immature fruits, 73% showed slight roughness on the surface of the fruit, 54% showed an intermediate thickness of the fruit wall, and 90% had the appearance of pairs of equidistant ridges. Regarding seed characteristics, 71% showed purplish cotyledons, with a high presence of floral and fruity notes and low levels of bitterness and astringency. Likewise, 52% of the fruits and 64% of the seeds were long. More importantly, cocoa beans needed to produce between 14 and 16 pods to obtain one kilogram of dry cocoa, which reflects a good level of productivity. Finally, there was a positive relationship between elevation levels and the presence of fine-flavoured native cocoa, i.e., the greatest diversity of native cocoa with floral and fruity notes was found above 501 metres above sea level.