Autothermal Thermophilic Aerobic Digestion (ATAD) is a technology for municipal waste water treatment where Class A Biosolids is produced. ATAD systems characteristic with the simplicity of the process, the higher reaction rate and smaller bioreactors. Systematic observations carried out on conventional ATAD systems have shown that their major disadvantage is the thermal shock that occurs in first bioreactors stages due to uncertainties regarding to the quantities, composition and temperatures of the incoming into the system raw sludge. This study focuses on opportunities for the thermal shock reduction in conventional ATAD system through recovery the heat from the effluent stream. It can lead to substantial savings of the time required for operating temperature recovery and quicker bio-degradation. To reduce the impact of the stochastic parameters and to ensure efficient using of the waste heat for the sustainable operation of the ATAD system, two mathematical models of energy integration with one and two heat storage tanks are proposed which will be suitable to be involved in a stochastic optimization framework.