During continuous operation of three mesophilic‐anaerobic digesters, the effect of microwave irradiation, as sludge thermal pretreatment (60 to 65°C), was studied. The fecal coliforms log inactivation for microwaved/digested sludge was 4.2 ± 0.4, whereas for conventionally heated/digested sludge and control were 2.9 ± 0.5 and 1.5 ± 0.5, respectively. In the case of Salmonella spp., no colonies were detected in 85% of the microwaved/digested samples. Considering the detection limit, the log inactivation of these samples was greater than 2.0 ± 0.3. The conventionally heated/digested sludge and control showed log inactivations of 1.9 ± 0.2 and 1.1 ± 0.3, respectively. 
 
 At the 95% confidence level, microwaved/digested sludge increased the biogas production by 16.4 ± 5.6% and 6.3 ± 2.4%, as compared to control and conventionally heated/digested sludge, respectively. When thermally treated sludge was analyzed for soluble chemical oxygen demand, microwaved waste‐activated sludge showed considerable solubilization between 37 and 60°C.
 
 Microwaved/digested sludge showed a reduction of capillary suction times by 11.1 ± 5.9% and 10.7 ± 5.6%, as compared to control and conventionally heated/digested sludge, respectively.