Peru is one of the main areas where there are large cocoa crops with special relevance to the economy of this country. In fact, cocoa is a major, economically important, international crop which has been linked to several benefits, such as anti-allergenic, anti-atherogenic, anti-inflammatory, anti-microbial, anti-oxidant, anti-thrombotic, cardioprotective and vasodilatory properties, relating to its bioactive compound content. However, in cocoa industrial processing, several residues or wastes, which are commonly discarded generating a negative impact on the environment, are produced in large amounts. Some of the cocoa by-products, which go underutilized, could be a good source of bioactive compounds with high utility for the development of innovative products in nutraceutical, medical or pharmaceutical industries. For this reason, the aim of this study is to qualitatively determine the phytochemical composition of husk and bean extracts from different cocoa-growing areas and processes from Peru by high performance liquid chromatography coupled to mass spectrometry. Furthermore, we aim to evaluate their phenolic and flavan-3-ol contents and antioxidant capacities for the purpose of highlighting the potential of cocoa by-products from these cultivars as functional ingredients. In total, 49 chemical compounds were detected in the analyzed extracts. Comparing both husks and beans, bean extracts were characterized by high content in flavonoids whereas husk extracts had a higher content of phenolic acids. The presence of these compounds together with the bioactivity results suggest that these matrices may be further studied for their revaluation in the development of high added-value products in nutraceutical, medical, and pharmaceutical industries.