Peru is home to six of the main genetic clusters of cocoa (Theobroma cacao L.) and is an important exporter of fine-flavor cocoa varieties. Two varieties of Peruvian native cocoa, in high demand for the fine chocolate market, grow in the regions of Bagua (Amazonas) and Quillabamba (Cusco). The main chemical and organoleptic characteristics of these two varieties were determined. Cocoa pastes and chocolates made with cocoa from these regions were subjected to chemical proximate analysis and determination of fatty acid profile, theobromine, caffeine, total phenolics, total flavonoids, antioxidant activity, and main sensory attributes. A multiple factor analysis (MFA) was applied to the data. Samples from Quillabamba differ from those of Bagua mainly by having a higher fat and lower theobromine content. The main sensory attributes detected for Bagua samples that differ from, those of Quillabamba were fruity, acidic, astringent, and bitter notes.