To investigate the sporicidal mechanisms of microwave irradiation on Bacillus licheniformis spores. We measured spore viability and the release of DNA and proteins, and performed transmission electron microscopy (TEM). A microwave oven (0.5 kW) was modified to output power at 2.0 kW, which allowed a shorter sterilization cycle. A 2.0 kW microwave treatment at the boiling temperature for 1 min did not kill all spores, but killed most spores. The spore inactivation rate was faster than that of boiling and 0.5 kW microwave oven. In contrast to boiling and 0.5 kW microwave treatments, the 2.0 kW microwave resulted in significant leakage of proteins and DNA from spores due to injury to the spore structure. TEM revealed that 2.0 kW microwave irradiation affected spore cortex hydrolysis and swelling, and ruptured the spore coat and inner membrane. These results suggest that 2.0 kW microwave irradiation ruptures the spore coat and inner membrane, and is significantly different from boiling. This study provides information on the sporicidal mechanisms of microwave irradiation on B. licheniformis spores.