This article is an outcome of the study, decisions, and restoration work undertaken during the integrated conservation project of the 16th century paintings of Funchal's Cathedral main chapel's altarpiece, in Madeira Island, Portugal. After diagnostic research has allowed a complete understanding of the original material of the 12 Portuguese-Flemish paintings, it has been revealed the presence of other superimposed layers, whether actual overpaints or the accumulation of materials occurring in time over the old ones. Identification together with the cleaning and removal of these coatings was a delicate and a complex process. Conservators already suspected the existence of overpaints in some paintings, a close observation of the painted surface showed differences in terms of color, texture, and execution technique in specific areas. Chemical and stratigraphical research together with radiography and historical research on primary documental sources provided important clues about the paintings of the previous interventions and relevant and crucial information for the decision making. (c) 2016 Wiley Periodicals, Inc. Col Res Appl, 41, 283-288, 2016