The often high Cd concentrations of cacao beans are a serious concern for producers in Latin America due to the implementation of stricter Cd limits for cocoa products by the European Union in 2019. This is the first investigation to employ coupled Cd isotope and concentration measurements to study soil – cacao systems. Analyses were carried out for 29 samples of soils, soil amendments and cacao tree organs from organic farms in Ecuador that harvest three distinct cacao cultivars. The majority of soils from 0–80 cm depth have very similar δ^114/110Cd of about −0.1‰ to 0‰. Two 0–5 cm topsoils, however, have high Cd concentrations coupled with heavy Cd isotope compositions of δ^114/110Cd ≈ 0.2%, possibly indicating Cd additions from the tree litter used as organic fertilizer. Whilst cacao leaves, pods and beans are ubiquitously enriched in Cd relative to soils there are distinct Cd isotope signatures. The leaves and pods are isotopically heavier than the soils, with similar Δ^114/110Cd_leaf–soil values of 0.22 ± 0.07‰ to 0.41 ± 0.09‰. In contrast, the data reveal differences in Δ^114/110Cd_bean–leaf that may be linked to distinct cacao cultivars. In detail, Δ^114/110Cd_bean–leaf values of −0.34‰ to −0.40‰ were obtained for Nacional cacao from two farms, whilst CCN-51 hybrid cacao from a third farm showed no fractionation within error (−0.08 ± 0.13‰). As such, further work to investigate whether Cd isotopes are indeed useful for tracing sources of Cd enrichments in soils and to inform genetic efforts to reduce the Cd burden of cocoa is indicated.