The aim of this study is application of an approach for solution of two-stage stochastic optimization problem for design of heat-integrated Autothermal Thermophilic Aerobic Digestion (ATAD) bioreactors system for municipal wastewater treatment operating under uncertainties. It incorporates in a common superstructure of two models of heat integration with one heat storage tank and two heat storage tanks for storing the heat used for preheating the incoming into the ATAD system cold raw sludge. On the first stage of the approach heat exchanger networks areas and the volumes of the heat storage tanks are determined. On the second stage - the flows rates represented by respective heating and cooling times are determined. As an optimization criterion - the annual capital costs for needed for the purpose of redesign of the ATAD system equipment as heat exchangers, heat storage tanks and pumps is determined as well as operating costs related with energy consumption of used pumps. The optimization problem is solved using genetic algorithm. Implementation of the proposed approach results in reduction of the depth of the thermal shock and achievement of sustainability improvement of the ATAD system.