The microwave insect extermination in wood is an effective treatment that has prospects for application in the field of heritage preservation. However, its use in polychrome wood should be studied in depth, to discover possible changes that may occur in the pictorial components. This article presents the studies performed to assess how egg tempera polychromies behave under microwave radiation. To do this, the heating of the binder and traditional pigments and the colour variations were studied. The treatment times and powers applied showed that despite the presence of metallic particles in many of the pigments, polychromies remain at values lower tham the wood’s heating, the colorimetric change obtained in the group of polychromies being found to be imperceptible.