Historically, cocoa (Theobroma cacao) has been one of Ecuador’s most important export crops. In the Ponce Enriquez district, artisanal and small gold mining (ASGM), and quarrying account for 42% of economic activities, while agriculture and livestock farming account for 30%, making the analysis of their synergy and interaction key to understanding the long term viability of the different activities. In this study, we evaluated the concentration of potentially toxic metals in different parts of the cocoa plant and fruit, in relation to mining activities within the area. Gold extraction generates pollution, including potentially toxic metals such as mercury (Hg), cadmium (Cd), arsenic (As), copper (Cu), lead (Pb) and zinc (Zn). In order to understand the mobility of these metals within the cocoa plant and fruit, the analysis was conducted separately for leaves, pod, husk and cocoa bean. Concentrations of the target metals in the different plant parts and soil were measured using ICP-MS, and the mobility and risk factors were calculated using the transfer factor (TF) and the risk ratio (HQ). The results suggest that Zn, Cd and Cu are indeed moving from the soil to cocoa leaves and beans. Furthermore, the results show that the concentrations of toxic metals in the different parts of the cocoa fruit and plant, particularly in the cocoa bean, which is used for chocolate manufacture, are not higher than those regulated by FAO food standards, as is the case of Cd, which is limited to 0.2 mg Cd/kg and in the samples analyzed does not exceed this limit. Even though the concentration of these metals does not exceed the safety standard, the presence of these potentially hazardous metals, and the fact they are absorbed by this important local crop, are worrying for the long-term sustainability of cocoa cultivation in the area. Therefore, it is fundamental to monitor the local environment, understanding the distribution of heavy metal pollution, and work with the local authorities in landscape management to minimize the exposure of crops to ASGM pollution.