Autothermal thermophilic aerobic digestion (ATAD) is an advanced sewage sludge treatment which allows compliance with increasingly demanding regulations. Concerning sludge pasteurization, a certain average temperature must be assured in the digester during batch treatment. Aeration flow is the variable most manipulated to regulate the digester temperature. Additionally, the manipulation of the batch sludge flow-which is related to the solid-retention-time-is considered to improve temperature regulation despite variations in air and sludge temperatures and the variability of raw sludge organic content. Thus, a dual-input control structure was provided where the aeration and solid-retention-time contributed as faster and slower inputs, respectively. Two controllers intervened, and the set-point for the batch average temperature was chosen to meet the minimum effluent quality established by the US regulations or European recommendations, considering that lower set point temperatures save aeration costs. A set-point for the aeration allowed us to achieve an extra goal, which aimed at either reducing operation costs or increasing production rates. The two feedback controllers were designed following the robust control methodology known as quantitative feedback theory (QFT). Improvements were compared with single-input (aeration-flow) control strategy and open-loop control strategy. Simulations were performed on a benchmark non-linear simulation model for ATAD.