In Venezuela, Criollo cacao crops are distributed in different regions (eastern, central and western), and under different exploitation systems, and, in each of these regions, there is a uniqueness of materials with characteristics associated to an intrinsic, differential quality that could potentially affect chocolate quality. These regions have inherent climates that are significantly different; however, there is a lack of consistent technical information about the real effects of environmental factors on the organoleptic quality of cacao. Therefore, the present work aims to evaluate the content of important components of cacao, such as phenolic compounds, lignin, amino acids, and carbohydrate, in six Theobroma cacao L clones, cultivated in three different agro-climatic locations: humid, semi-humid and dry tropical forest. It was found that production of phenolic compounds and lignin vary in clones according to their location, with the highest values found in the humid forest and the lowest in the dry climate. Non-structural carbohydrates, on the other hand, were found in greater amounts in specimens from the dry forest. The largest production of proline was found in the humid forest for most of the clones, implying that high humidity levels promote the production of amino acids, a pattern followed by phenolic compound content as well. The results presented in this study indicate that there is a climate-dependent production of important metabolites, which play an important role in the organoleptic properties of cacao, and this could potentially translate into different levels of resistance to stress and diseases.