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More and more attention is paid to sustainability in the cocoa production. Tools that assist in making sustainable cocoa traceable are therefore welcome. In the present study, the applicability of Flow Infusion-Electrospray Ionization- Mass Spectrometry (FI-ESI-MS) to assess the geographical origin of cocoa beans used to produce chocolate has been tested. Fifty-seven dark chocolates available on the Dutch market were investigated taking into account the geographical origin of the beans: they originated from Africa (15), Asia (11) and South America (31). The FI-ESI-MS generated non-volatile profiles, were subjected to ANOVA selection (21 masses per sample). Those were subsequently used as fingerprints and investigated using chemometric tools to elucidate information on raw material origin. Principal component analysis revealed a remarkable separation between African and Asian bean chocolates. No clear trend was observed for the chocolates manufactured from South American beans. The kNN results confirmed the possibility to separate African and Asian chocolates as well as these two continents together versus the South America. The inability to separate the three continents at the same time and the weak differentiation of South American samples from the others is linked to brand-related factors, such as the formulation and industrial processing. Although diminishing of the influence of the brand-related factors will improve separation, the current approach is an important step in the geographical assessment of the raw material and the traceability of cocoa in its supply chain.