The cocoa varieties Criollo, Forastero and Trinitario, which have different organoleptic properties, quite often are mixed together in cocoa-based products. The objective of this work was to develop a rapid method for the simultaneous determination of polyphenols (n = 35) and alkaloids (n = 2) in cocoa-based products by using the high throughput advantages provided by the Q Exactive Hybrid Quadrupole-Orbitrap Mass Spectrometer (HRMS). The proposed procedure was optimized and validated in terms of selectivity and specificity (mass accuracy <5 ppm), sensitivity (instrumental limit of detection from 15 to 30 fg), linearity (r > 0.990), accuracy (recovery range from 89.1 to 112.4%) and precision (relative standard deviation <10%). The method was applied to 80 cocoa-based samples. Alkaloids represented on average the 57.7% of assayed compounds. Flavanols and procyanidins were the most abundant polyphenols being quantified in a range between 261 and 668 mg/kg and from 127 to 405 mg/g, respectively. Mass equivalents but structural isomers bioflavonoids were characterized by using the HRMS-Orbitrap methodology here developed.