Cocoa represents a crucial source of income in coastal regions of Ecuador, where the product is exported for the production of high-value chocolates. However, elevated levels of cadmium (Cd) in cocoa beans, attributable to volcanic soils, have the potential to impede international trade, particularly in accordance with European Union regulations. The main objective of this study was to reduce Cd concentrations in cocoa beans of two genotypes, Nacional and CCN-51, by applying different doses of pectin trans-eliminase (PTE) enzyme during the fermentation process in conjunction with mucilage washing techniques, pre-drying resting periods, and various drying methods. To this end, a Taguchi orthogonal design (L9) was employed to evaluate nine treatments per genotype, complemented with two controls. The most efficacious treatment for Nacional was identified as T7, involving a 0.30 mL·kg⁻¹ PTE dose, the absence of mucilage washing, a 48 h resting period, and drying in a marquee. This treatment resulted in a 68.6% reduction in Cd concentration (from 0.28 to 0.09 mg·kg⁻¹). For CCN-51, T3 (0.10 mL·kg⁻¹ PTE, complete washing, 48 h resting, and splint drying) yielded a 26.4% reduction in Cd (from 0.42 to 0.31 mg·kg⁻¹). It is noteworthy that none of the treatments exceeded the EU regulatory threshold of 0.8 mg·kg⁻¹. A physico-chemical analysis was conducted, which revealed significant treatment effects on pH (ranging from 5.63 to 6.85) and acidity (0.02% to 0.03%). Sensory evaluation indicated enhancements in cocoa and nutty flavors, along with a reduction in undesirable astringency and bitterness, particularly in Nacional samples. The findings of this study demonstrate that the combination of enzyme-assisted fermentation and optimized postharvest techniques represents a pragmatic approach to the mitigation of cadmium in cocoa, while simultaneously preserving or enhancing product quality.