The aim of this paper is to establish and quantify different operational goals and control strategies in autothermal thermophilic aerobic digestion (ATAD). This technology appears as an alternative to conventional sludge digestion systems. During the batch-mode reaction, high temperatures promote sludge stabilization and pasteurization. The digester temperature is usually the only online, robust, measurable variable. The average temperature can be regulated by manipulating both the air injection and the sludge retention time. An improved performance of diverse biochemical variables can be achieved through proper manipulation of these inputs. However, a better quality of treated sludge usually implies major operating costs or a lower production rate. Thus, quality, production and cost indices are defined to quantify the outcomes of the treatment. Based on these, tradeoff control strategies are proposed and illustrated through some examples. This paper's results are relevant to guide plant operators, to design automatic control systems and to compare or evaluate the control performance on ATAD systems.