The transesterification reaction catalyzed by dibutyltin oxide has been used to crosslink miscible blends (at about 200-degrees-C) of ethylene vinyl acetate (EVA) and ethylene methyl acrylate (EMA) copolymers. Then, microwave heating at 2.45 GHz with the fundamental TE01 mode was used for activation of this crosslinking reaction. The microwave treatment was carried out in a continuous process through a resonant cavity on line with a twin screw extruder equipped with a strip die or a circular die, which imposed the shape of the samples in the waveguide. Therefore, a shape factor due to the geometry of the samples and their orientation with respect to the electromagnetic field was defined. Last, this technique was applied to the microwave crosslinking of an EVA/EMA blend dispersed in a polypropylene matrix and consequently offers a new route to control the morphology of the polymer blends.