A method for processing articles, the method comprising: accessing an operating profile (302a-n) for heating a type of article using a microwave heating system, the operating profile (302a-n) including a first group of set point values for operating the microwave heating system to heat the type of article according to a first heating process and a second group of set point values for operating the microwave heating system to heat the type of article according to a second heating process different than the first heating process; and using a control system operatively coupled to the microwave heating system, operating the microwave heating system according to the first group of set point values, the first group of set point values including a target value for a control parameter of the microwave heating system, wherein operating the microwave heating system includes: passing a carrier loaded with a plurality of articles of the type of article corresponding to the operating profile (302a-n) through a liquid-filled microwave heating chamber along a convey line such that the plurality of articles is submerged in a liquid medium within the microwave heating chamber; and while passing the carrier through the microwave heating chamber, discharging microwave energy into the microwave heating chamber, the microwave energy used to heat the plurality of articles; measuring the control parameter to provide a measured value; calculating a difference between the measured value and the target value; and responsive to determining the difference exceeds a predetermine allowable difference, operating the microwave heating system according to the second group of set point values. accessing an operating profile (302a-n) for heating a type of article using a microwave heating system, the operating profile (302a-n) including a first group of set point values for operating the microwave heating system to heat the type of article according to a first heating process and a second group of set point values for operating the microwave heating system to heat the type of article according to a second heating process different than the first heating process; and using a control system operatively coupled to the microwave heating system, operating the microwave heating system according to the first group of set point values, the first group of set point values including a target value for a control parameter of the microwave heating system, wherein operating the microwave heating system includes: passing a carrier loaded with a plurality of articles of the type of article corresponding to the operating profile (302a-n) through a liquid-filled microwave heating chamber along a convey line such that the plurality of articles is submerged in a liquid medium within the microwave heating chamber; and while passing the carrier through the microwave heating chamber, discharging microwave energy into the microwave heating chamber, the microwave energy used to heat the plurality of articles; passing a carrier loaded with a plurality of articles of the type of article corresponding to the operating profile (302a-n) through a liquid-filled microwave heating chamber along a convey line such that the plurality of articles is submerged in a liquid medium within the microwave heating chamber; and while passing the carrier through the microwave heating chamber, discharging microwave energy into the microwave heating chamber, the microwave energy used to heat the plurality of articles; measuring the control parameter to provide a measured value; calculating a difference between the measured value and the target value; and responsive to determining the difference exceeds a predetermine allowable difference, operating the microwave heating system according to the second group of set point values.