ABSTRACT:In recent years there has been a growing interest in cocoa and their sub products in the world, given the beneficial properties of these products. This interest has led to increased research in the study of the composition of cocoa and its relationship with its varieties, mainly the principal alkaloids, theobromine and caffeine. Venezuela, although a small‐scale producer, is recognised worldwide for the quality of its cocoa. This work presents a robust, unambiguous and cost‐effective methodology for the rapid and accurate quantification of theobromine and caffeine in cocoa beans extracts from Venezuelan cocoa. Thin layer chromatography (TLC) is used for separation, and alkaloids are identified by their Rf values and by their Raman spectra obtained by surface‐enhanced Raman spectroscopy (SERS). In the SERS technique, the spots of separated compounds by TLC were impregnated with a solution of silver nanoparticles and the SERS spectra record. Given the great structural similarity of these alkaloids, principal component analysis (PCA) was used to show that despite the similarities of the Raman spectra, they are perfectly distinguishable. Theoretical calculations were performed using Orca software, obtaining Raman and FTIR spectra, and similarities were found between the theoretical and experimental responses, validating the computational approach. The synergistic integration of TLC for separation, SERS for sensitive detection, PCA for robust differentiation and DFT for theoretical validation offers a cost‐effective, rapid and robust analytical platform for the unambiguous identification of theobromine and caffeine in complex matrices. This methodology lays the foundation for future quantitative applications in the evaluation of cocoa quality and origin.