Accurate temperature measurement during any microwave processing of material is a contentious issue. While thermocouples are routinely utilized in conventional heat furnaces, their presence in microwave cavities may cause complications such as localized distortion of electromagnetic field, heat dissipation, thermal instabilities, microwave breakdown, and significant inaccuracies in temperature measurement. Therefore, in the present investigation thermocouple effects are discussed by providing the results of temperature estimation by various thermocouples for microwave cladding systems. The present study theoretically and experimentally explored the impact of multiple thermocouples on temperature measurements during microwave heating. COMSOL simulation models were developed to explore microwave and thermocouple interaction during microwave heating. Simulation models were used to assess the effects of the microwave power intensity, thermocouple orientation, and geometry on temperature measurement. The investigation outcomes can be utilized as a guide for selecting appropriate thermocouples in the applications of microwave cladding and other microwave-based manufacturing processes.