In Ecuador, the cultivation of two main coffee species, Coffea arabica L. and Coffea canephora L., holds significant economic, environmental, social, and public health importance. C. arabica displays wide adaptability to diverse growing conditions, while C. canephora exhibits less versatility in adaptation but is superior in metabolite production in the ripe fruits (with the potential to double caffeine content). Our hypothesis revolves around the differences in the production of secondary metabolites, antioxidant capacity and sensory attributes based on the environmental conditions of the two studies species cultivated in Ecuador. The assessment of the metabolic composition of high-altitude coffee grown in Ecuador involved the determination of secondary metabolites and quantification of the antioxidant capacity through the 2,2-diphenyl-1-picrylhydrazyl assay, 2,2′-azino-bis (3-ethylbenzothiazoline-6-sulfonic acid) quenching assay, and ferric reducing antioxidant power assay. In the case of C. arabica, a high positive correlation was observed for total phenolic content (TPC) (4.188 ± 0.029 mg gallic acid equivalent (GAE)/g dry weight (dw)) and total flavonoid content (TFC) (0.442 ± 0.001 mg quercetin (QE)/g dw) with the antioxidant activity determined through ABTS free-radical-scavenging activity (23.179 ± 1.802 µmol Trolox (TEAC)/g dw) (R = 0.68), a medium correlation with DPPH^• radical-scavenging activity (65.875 ± 1.129 µmol TEAC/g dw) (R = 0.57), and a low correlation with ferric reducing antioxidant power assay ((100.164 ± 0.332 µmol Fe²⁺/g dw) (R = 0.27). A high correlation (R > 90) was observed for the values evaluated in the case of C. canephora. The caffeine content was high in C. arabica beans from Los Ríos province and in C. canephora beans from Loja.