Abstract Exergy transfer analysis is proposed as a complementary method for analyzing and better understanding of the efficiency of microwave heating systems, which play a key role in medicine, chemical engineering, food industry and material processing. Since this method is able to detect and quantify in detail where irreversibilities occur, it can be a useful first step in the improvement of microwave systems. First, the different approaches for modeling microwave systems and interactions wave-thermal system are reviewed. Then, relation between Poynting vector, energy and exergy in microwaves is analyzed in depth. Afterwards, a 2-D model of energy and exergy transfer for a microwave heating system is presented. The model is based on Lambert's Law and is applied for the analysis of a potato heating. A comparison with a conventional heating is also presented, where the irreversibility evolution of both process, microwave and conventional, is analyzed with the presented methodology, presenting advantages and disadvantages for each process. This simple example proposed for illustration demonstrates how the analysis of exergy transfer results allows one not only to characterize the global exergy efficiency of the system but also analyze in depth the time and space distribution of exergy flows, exergy variation and irreversibility.