A simplified model of the microwave-assisted combustion synthesis of Ni and Al metal powders to form the NiAl intermetallic on titanium and steel substrates is presented. The simulation couples an electro-thermal model with a chemical model, accounting for local heat generation due to the highly exothermic nature of the reactions between the powders. Numerical results, validated by experimental values, show that the capability of microwaves to convey energy, and not heat, can be used to alter the temperature profiles during and after the combustion synthesis, leading to unique intermetallic microstructures. This phenomenon is ascribed to the extended existence of high temperature liquid intermetallic phases, which react with the metallic substrates at the interface. Moreover, microwave heating selectivity allows to maintain the bulk of the substrate metallic materials to a much lower temperature, compared to combustion synthesis in conventionally heated furnaces, thus reducing possible unwanted transformations like phase change or oxidation.