The study investigated the effect of adding citrus fruits on the dynamics of reducing sugars during the fermentation of Criollo cocoa beans from Lagunas and Casual (Amazonas, Peru). Both spontaneous fermentations and fermentations supplemented with orange, passion fruit, or pineapple at concentrations of 5% and 10% were conducted over six days in wooden boxes, with samples collected every 24 h. Sucrose, glucose, and fructose contents were quantified using ultra-high-performance liquid chromatography coupled with a refractive index detector (UHPLC-RID), and the data were analyzed via ANOVA and PCA. In samples from Lagunas, initial sucrose levels (69.22 mg/g) decreased sharply during the first two days, whereas in the fermented mass from Casual, the sucrose concentrations were low from the outset (6.3 mg/g). The addition of citrus fruits promoted higher accumulation of glucose and fructose in the intermediate and final stages, reaching maximum concentrations of 76.24 mg/g and 81.06 mg/g, respectively, on day six in Lagunas with 10% fruit supplementation. Multivariate analysis indicated that fruit-treated fermentations exhibited a more active and distinct fermentation profile compared to spontaneous fermentations. These results demonstrate that the controlled addition of citrus fruits represents an innovative, low-cost biotechnological strategy for optimizing cocoa fermentation and may enhance the development of flavor and aroma precursors.