A generalized matrix method to treat multilayer systems with mixed coherent and incoherent optical behavior is presented. The method is based on the calculation of the light energy flux inside the multilayer, whose internal light absorption is straightforwardly derived. The Poynting vector is used to derive the light energy flux in the case of a layer with coherent behavior. Multilayer structures with any distribution of layers with coherent or incoherent behavior can be treated, including the case of oblique incidence. Use of the light energy flux instead of the more commonly used light intensity permits the calculation of light absorption with a better accuracy and a much shorter computation time.