Cadmium (Cd) is a non-nutritive element present across the earth. In cacao crops from South America, Cd has become one of the biggest challenges due to its flux from soils, and due to the enriched content of this metal, it makes its way into the beans and finally affects the chocolate quality. This manuscript aims to show how the flux of Cd occurs, from the soil to the post-harvest phase and chocolate production, by analysing the possible inputs to the system in a single farm assessed as a model for enriched-Cd status. This study shows that both geogenic and anthropogenic activities have an incidence on the final Cd content in chocolate, especially with respect to soil properties, fertiliser applications, post-harvest treatments and chocolate production.