The whey is a byproduct of the dairy industry that, if not treated properly, can cause serious environmental pollution problems. Anaerobic treatment is an alternative for its recovery, since, in addition to reducing the organic load. it allows the generation of value-added products such as volatile fatty acids (VFA) and biogas. However, the process is very complex and requires specific operating conditions that guarantee its stability and favor the production of value-added compounds. In this work, an unstructured mathematical model is proposed to evaluate the dynamic behavior of the stages of the anaerobic degradation process of the whey (i.e., hydrolysis, acidogenesis, acetogenesis and methanogenesis). The proposed model considers the dynamic variation in pH during the experiment. To validate the model, an experimental set was carried out at pH and temperature conditions that favor the production of VFAs. Experimental results show that the anaerobic treatment of the raw cheese whey favors pH = 5.5; for T = 40 °C, the maximum VFA production is obtained (30.71 gCOD L−1), and for T = 35 °C, a 45.81% COD degradation is reached. The proposed model considers the effect of pH and temperature and it is validated in the region where the experimental tests were carried out. The model parameters were estimated using the Levenberg−Marquardt method, obtaining coefficients of determination R2 > 0.94. The proposed model can describe the dynamic behavior of the key variables in the anaerobic treatment of raw cheese whey at different pH and temperature conditions, finding that VFA production is favored at pH ≥ 7, while the highest COD removal results in acidic conditions