The presented study describes the deterioration of a traditional pigment, malachite—[Cu2(CO3)(OH)2] in different binders, as a consequence of environmental effects acting on paint layers which were prepared according to traditional Baroque recipes. Malachite has often been reported to be very permanent in all binding media; however, investigations of aged and nonaged paint layers by means of Raman microscopy have shown instability of the carbonate part of the molecule, especially when malachite is present in an egg yolk medium. Decomposition of the pigment and the formation of degradation products such as copper oxide (tenorite—CuO) were observed. The possible formation of another copper oxide, paramelaconite—Cu4O3 was also taken into consideration. In order to obtain additional information on the degradation processes which affect malachite paint layers, supporting analytical methods, such as scanning electron microscopy and X-ray diffraction, were used.