Cocoa flavour is achieved during the physicochemical transformation of seeds through postharvest operations. To ensure adequate conditions for the reactions involved with the formation of flavour precursors, it is highly favourable to control operational variables. This study evaluates the effect of organic acids (acetic, lactic, and citric acids) and the physicochemical conditions of the process (organic acid concentration, temperature, stirring rate, and solid–liquid ratio) on the mass transfer phenomena and the formation of reducing sugars. Fick's second law modelled the mass transfer of organic acids into the seed. The effective diffusivity and the mass transfer coefficients depended on the organic acid used in the controlled transformation. All the operational variables evaluated were statistically significant in the mass transfer of lactic and citric acids, while the concentration was not significant for acetic acid. The organic acid concentration influenced the reducing sugar content in the cocoa beans in the acetic acid trials, while both the concentration and the temperature influenced the reducing sugar content in the lactic and citric acid trials. This study is a first step in defining contour limit values of the operational variables that control the transformation of cocoa seeds, leading to its optimisation and, ultimately, the scale-up process.