An engineering foundation is developed in this manuscript to allow the rational design of enzymatic transesterifications integrated with organic–organic pervaporation for the removal of methanol. In the first part, enzyme kinetics are elucidated for the solventless transesterification of two monoterpene alcohols with methyl acetate catalyzed by Novozym 435. Nonlinear regression revealed that three parameters (enzyme loading, forward and backward second-order reaction rate) sufficed to describe the entire conversion as a function of time. In the second part, a mathematical model for acetate ester production, integrated with organic–organic pervaporation, was developed based on a set of ordinary differential equations. To this end, empirical formulae for the pervaporation performance (of a PERVAP 2255-30 membrane and a standard HybSi® membrane) were established, relating methyl acetate and methanol flux to the methanol concentration in the reactor. The resulting digital twin, “PervApp”, allows us to study the influence of the key design parameters “enzyme loading” and “membrane surface” on, e.g., catalyst productivity. Finally, a techno-economic assessment is made for an annual production of 100 tons of geranyl acetate. The described methodology allows producers to shift from laborious, expensive and often disappointing trial-and-error approaches to the rational design of such integrated units.