This paper describes a mathematical model for the convection, diffusion, and balance phenomena for predicting the depletion curves, i.e., variations in the timed surface-active molecule concentration for fractionation processes in bubbles and foam column, operated in semi-batch. The model was applied for the purification of the surfactin solution and the results were compared with experimental data. Gibbs adsorption curves were obtained for the biosurfactant at different temperatures, and then adjusted with estimated parameters, according to the Langmuir adsorption model. The gas bubble sizes were optically determined. The isotherm adsorption parameters and bubble average diameter are crucial for the attainment of the depletion curves, generated by the model described. The results demonstrate that the process is most effective when operating a column with reduced gas flow and low initial concentration. A top product with two or thirty times greater concentration than the initial one was achieved and the highest biosurfactant concentrations were attained for higher operating temperatures. It was also observed that bubble diameter increased with a higher gas flow. The adjustment obtained for the adsorption curves of Gibbs was satisfactory. Therefore, there was evidence that surfactin molecules adsorb in monolayers in the liquid–gas interface.