Present study proposes a methodology for energy efficiency and sustainability improvement of the operating conditions of batch production systems. The methodology is applied a conventional system for municipal wastewater treatment using the process of Autothermal Thermophilic Aerobic Digestion (ATAD) of sludge. Its sustainable operation is essential for the quality of the treated sludge and the reduction of environmental impact. An analysis of the possibilities for energy integration of processes in ATAD systems has been made. Structures for indirect energy integration of processes using storage tanks and mathematical models for describing energy integration for the studied object have been proposed. The models are included within a two-stage stochastic optimization problem together with constraints on the physical, technical and technological feasibility of the integration frameworks and temperature constraints with an optimization criterion minimum redesign cost. The obtained results show significant energy savings as a result of energy integration and sustainability to temperature conditions in bioreactors.