The present study proposes a decision-making approach based on flexibility index calculation of already obtained solutions of a stochastic multi-scenario optimization model for redesign of heat-integrated two-stage Autothermal Thermophilic Aerobic Digestion (ATAD) bioreactors system for municipal wastewater treatment operating under uncertainties. Obtained solutions with minimal costs for redesign were presented in Vladova et al. (2018). Aiming to find the solution which provides sustainable operation of the heat-integrated ATAD system within the widest range of variation of its uncertain parameters, the Flexibility Index (FI) approach should be applied. A fast approach for evaluation of the flexibility index by presenting it as an inscribed a hyper-rectangle in the scaled hyper-space of variation of the uncertain parameters so as to ensure no violation of the process feasibility constraints is proposed. An optimization problem for determining the maximal flexibility index is formulated and solved for each solution obtained in Vladova et al. (2018). Decision making is carried out to choose most sustainable solutions for redesigned ATAD system. Analyzing the results obtained, it can be concluded that not always the solutions with the minimal annual costs for redesigning provide the sustainable operation of the ATAD system.