A system and method for supplying microwave energy to tissue for microwave therapy includes an electrosurgical generator having an output for coupling to a surgical instrument. The electrosurgical generator includes a microwave energy source and a controller for controlling the operation of the electrosurgical generator. The surgical instrument, coupled to the electrosurgical generator, includes a microwave antenna for delivering microwave energy from the microwave energy source. The controller of the electrosurgical generator is operable for causing the electrosurgical generator to apply at least two pulses of microwave energy.