Acid and bitter notes of the cocoa clone Cacao Castro Naranjal 51 (CCN 51) negatively affect the final quality of the chocolate. Thence, the fermentative process of cocoa beans using native species and electromagnetic fields (EMF) was carried out to evaluate the effect on the yield and quality of CCN 51 cocoa beans. The variables magnetic field density (D), exposure time (T), and inoculum concentration (IC) were optimized through response surface methodology to obtain two statistically validated second-order models, explaining 88.39% and 92.51% of the variability in the yield and quality of the beans, respectively. In the coordinate: 5 mT(D), 22.5 min (T), and 1.6% (CI), yield and bean quality improved to 110% and 120% above the control (without magnetic field). The metagenomic analysis showed that the changes in the microbial communities favored the aroma profile at low and intermediate field densities (5-42 mT) with high yields and floral, fruity, and nutty notes. Conversely, field densities (80 mT) were evaluated with low yields and undesirable notes of acidity and bitterness. The findings revealed that EMF effectively improves the yield and quality of CCN 51 cocoa beans with future applications in the development and quality of chocolate products.