Cocoa (Theobroma cacao, L.) represents an important market that gained relevance and became an esteemed commodity thanks to cocoa powder, chocolate, and other related products. This work analyzed 59 cocoa powder samples from the European market. Three distinct subgroups were identified: organic or conventional, alkalized or not alkalized, and raw or roasted processing. The impact of the technological process on their pH, color, and compositional traits, as well as their content of biogenic amines and salsolinol, was evaluated. The phenolic fraction was also investigated through both common and emerging methods. The results depict that the influence of the agronomical practices (organic/conventional) did not significantly (p < 0.05) affect the composition of the cocoa powders; similarly, the roasting process was not a determinant of the compounds traced. On the other hand, the alkalinization process greatly impacted color and pH, no matter the cocoa’s provenience or obtention or other processes, also resulting in reducing the phenolic fraction of the treated samples. Principal component analysis confirmed that the alkali process acts on pH, color, and phenolic composition but not on the content of other bioactive molecules (biogenic amines and salsolinol). All the samples were safe, while the alkalized powders saw a great reduction in beneficial biocompounds. A novel strategy could be to emphasize on the label whether cocoa powder is non-alkalized to meet the demand for more beneficial products.
