This viewpoint discusses the possibility of developing stochastic models in food and bioproducts processes based on the thermodynamic properties of the involved molecules and particularly a generalized approach of Boltzmann entropy equation (S=k·lnW). To this line, enzyme kinetics modeling is discussed as a bioengineering practice to explore relationships between processes, structures and functions in food products, prior describing the macro- and micro-states according to Boltzmann entropy equations. Thereafter, two case studies (starch hydrolysis and β-glucan microstates) that followed this approach are critically revised. Finally, the possibility of applying this concept in modeling efforts of other applications in bioproducts processing, food industry, and food waste recovery are highlighted.