In this paper the equilibrium properties of the proline catalyzed aldol reaction was studied. The use of well-established methodologies, like reaction progress kinetic analysis and linear free energy relationship analysis, led to the quantification of the reaction reversibility and to its correlation with the substrate electronic activation. Due to these experimental observations, common computational approaches based on a one way transition state analysis become unsuitable. Therefore, a computational model based on the integration of a system of kinetic differential equations associated to the multiple equilibrium reactions was proposed. Such a model was found to successfully rationalize the chemical and stereochemical outcomes of this paradigmatic reaction for the first time.