Plants, including most food and feed plants, produce a broad range of bioactive chemical compounds. Among these compounds, polyphenols are reported to provide beneficial effects as anti-carcinogenic, anti-atherogenic, anti-inflammatory, immune modulating, anti-microbial, vasodilatory and analgesic. Cocoa (Theobroma cacao), a major, economically important, international crop, has been related to several nutritional benefits, which have been associated with the phenolic fraction. The main subclass of flavonoids found in cocoa is flavanols, particularly (epi)catechins monomers, and their oligomers, also known as procyanidins. In this study, these compounds were isolated by different methodologies as solid phase extraction (SPE), semi-preparative high-performance liquid chromatography (HPLC) and membrane technologies to obtain different polyphenolic profiles by HPLC coupled to electrospray time-of-flight mass spectrometry (ESI-TOF-MS) and to test their cytotoxicity. Finally, different polyphenolic profiles were collected, where the combination of both semi-preparative HPLC and SPE technologies provided the most purified fractions. Filtration with membranes and SPE provide extracts with different composition depending on the pore size of membranes and on the solvent, respectively. In addition, the results of toxicity assay indicated low levels in all fractions.