We present the results of using Raman molecular imaging and atomic force microscopy (AFM) investigation of the composition, stability, and photodegradation of polyelectrolyte multilayer microcapsules and coated microparticles containing copper–phthalocyanine and iron–phthalocyanine. The influence of laser light on degradation of these phthalocyanine dyes embedded in the walls of polyelectrolyte multilayer capsules and shells of microparticles was studied by both AFM and Raman molecular imaging, but only the latter technique gave information on dynamics of photodegradation. Raman peak assignment was performed according to theoretical calculations. The degradation rate of phthalocyanine dyes is estimated from Raman signal measurements and a model is proposed to account for the degradation rate. Practical applications of our approach are outlined. Copyright © 2011 John Wiley & Sons, Ltd.