In Ecuador, since 2005 in the northern Amazon, trinitario hybrid cacao mother plants characterized by early and abundant fruiting, known as “Super árbol”, have been identified. This genetic material was disseminated in the region, but most of the available information corresponds to empirical knowledge. In this sense, the present study aimed to evaluate different fermentation techniques in the “Super árbol” cocoa by analyzing physical and chemical variables in the climatic conditions of the Joya de Los Sachas canton to establish differences between the group of genetic material of the “Super árbol” cocoa with respect to the “Arriba” variety, which is considered a reference in Ecuador. The physical and chemical parameters evaluated were: fermentation rate, weight of 100 beans, pH cotyledon, beans shell, protein, ash, lipid, and total polyphenols. The study was conducted under a completely randomized design with three factors. A Spearman correlation analysis was performed, followed by the establishment of a model for each variable and the use of Tukey’s test to establish the difference between means of treatments and a Levene’s test to test homogeneity. The “Super árbol” cocoa reported fermentation percentages between 64.33 and 95%, testa percentages between 13.28 and 18.08%, and polyphenol content between 48.46–55.54 GAE/g DW. Thus, this genetic material of the “Super árbol” trinity group has characteristics that reach higher fermentation percentages compared with the “Arriba” variety. In addition, it has a lower polyphenol content (less bitter and astringent), which leads to a better-quality raw chocolate material.