Models of increasing complexity were developed to identify and represent mechanisms affecting the evolution of the concentration of 3 aroma compounds (2-phenylethanol, isoamyl acetate and butanal) usually produced by yeasts and transferred to coffee beans during the fermentation. Model parameters were identified from simulated wet treatment performed with four media (M1: dehulled beans, M2: demucilaginated beans, M3: depulped beans, M4: depulped beans with yeast), at 25 °C using labeled aroma compounds. The transfer of 2-phenylethanol was well described by a model including evolving resistance over time (R2 = 0.98) while the accumulation of isoamyl acetate and butanal was better described by a model including two first order reactions in parallel (r2 = 0.87–0.66 and r2 = 0.80–0.67, respectively). The model development contributed to understand several mechanisms involved during fermentation such as the evolutive parchment resistance and the complex degradation reactions that take place simultaneously and have a significant impact on the compounds transfer.