BACKGROUND Invertase use in the food industry is limited by production costs. Alternative strategies for extraction, such as aqueous two‐phase systems (ATPS) and three‐phase partitioning (TPP), could be economically feasible for yeast invertase. Economic modeling of bioprocesses makes possible the identification of critical parameters for production costs and emulation of real scenarios, moreover incorporation of uncertainty is possible. This study performed an economic analysis on the production of invertase using ATPS or TPP, also a virtual optimization of ATPS was done. RESULTS TPP provided a lower production cost than ATPS ($145 vs $59.3 per 1 million enzymatic units, respectively). The critical parameter for TPP is recovery yield as it is highly dependent on operating conditions. In contrast, ATPS is dependent on materials costs as the sample load is smaller for ATPS, requiring a larger system. Although TPP provided a lower cost, t‐butanol hinders its acceptance. CONCLUSION Virtual optimization of ATPS found that varying sample load or system size is not enough to have a lower production cost than TPP, but provided insights for reduction of production costs and development of a safer technique. This study provides a framework for the virtual analysis of ATPS and TPP to evaluate their processes and reduce production costs. © 2018 Society of Chemical Industry