Plants, including cocoa bean, are the main source of metabolites with multiple biological functions. Polyphenol extracts are widely used as a nutraceutical supplement for their well‐known health‐promoting role. In this paper, a preliminary untargeted metabolic screening was carried out by matrix‐assisted laser desorption/ionization (MALDI)‐time of flight (TOF)/TOF on a pool of chocolate samples made by cocoa beans of different geographical areas. Then, a targeted approach was developed for polyphenol quantification by an optimized Liquid chromatography (LC)–tandem mass spectrometry (MS/MS) method multiple reaction monitoring (MRM) ion mode. Detection limit of polyphenol standard ranged between 1 and 25 pg/μl with variation coefficient lower than 15%. External calibration curves were used for quantification of polyphenols in 18 samples. Fifty polyphenols were detected in a single LC–MRM/MS run and quantified by monitoring almost 90 transitions in a 5‐minute run. The polyphenols content of different cocoa beans from several countries was finally compared by principal component analysis (PCA) statistical analysis suggesting that the chocolate made by Ecuador cocoa beans showed the highest level of polyphenols.