Abstract Pretreatment of thickened waste activated sludge (TWAS) by combined microwave and alkaline pretreatment (MAP) was studied to improve thermophilic anaerobic digestion efficiency. Uniform design was applied to determine the combination of target temperature (11 degrees-210 degrees C), microwave holding time (1-51 min), and NaOH dose (0-2.5 g NaOH/g suspended solids (SS)) in terms of their effect on volatile suspended solids (VSS) solubilization. Maximum solubilization ratio (85.1%) of VSS was observed at 210 degrees C with 0.2 g-NaOH/g-SS and 35 min holding time. The effects of 12 different pretreatment methods were investigated in 28 thermophilic batch reactors by monitoring cumulative methane production (CMP). Improvements in methane production in the TWAS were directly related to the microwave and alkaline pretreatment of the sludge. The highest CMP was a 27% improvement over the control. In spite of the increase in soluble chemical oxygen demand concentration and the decrease in dewaterability of digested sludge, a semi-continuous thermophilic reactor fed with pretreated TWAS without neutralization (at 170 degrees C with 1 min holding time and 0.05 g NaOH/g SS) was stable and functioned well, with volatile solid (VS) and total chemical oxygen demand (TCOD) reductions of 28% and 18%, respectively, which were higher than those of the control system. Additionally, methane yields (L@STP/g-CODadded, at standard temperature and pressure (STP) conditions of 0 degree C and 101.325 kPa) and (L@STP/g VSadded) increased by 17% and 13%, respectively, compared to the control reactor.