Autothermal Thermophilic Aerobic Digestion (ATAD technology) is a promising alternative to conventional digestion systems. Aeration is a key factor in the performance of these kinds of reactors, in relation to effluent quality and operating costs. At present, the realisation of automatic control in ATADs is in its infancy. Additionally, the lack of robust sensors also makes the control of these processes difficult: only redox potential and temperature sensors are reliable for operation in full-scale plants. Based as it is on the existing simulation protocols for benchmarking of control strategies for wastewater treatment plants (WWTP), this paper presents the definition and implementation of a similar protocol but specifically adapted to the needs of ATAD technology. The implemented simulation protocol has been used to validate two different control strategies for aeration (ST1 and ST2). In comparison to an open-loop operation for the ATAD, simulation results showed that the ST1 strategy was able to save aeration costs of around 2–4%. Unlike ST1, ST2 achieved maximum sludge stabilisation but at the expense of higher aeration costs.