This study demonstrates the applicability of Raman spectroscopy, assisted with X‐ray fluorescence and scanning electron microscopy–energy dispersive X‐ray spectroscopy analyses, in the characterization of biominerals accumulated on several stone materials colonized by saxicolous lichens under different environmental conditions. The distribution of the diverse biominerals through the lichen–stone interface is described. Among them, neogenerated biominerals involved in the metabolism of Caloplaca and Lecanoraceae lichen genera such as calcium oxalates in their two hydrated forms were found in different parts of the lichen, even on sandstones that X‐ray spectroscopy evidenced the absence of calcium in their mineralogical composition. Hence, it is demonstrated the atmospheric intake likely as particulate matter composed of calcite. The occurrence of the calcium oxalates is shown not to be related to the environmental conditions but to the lichen genera, because no common patterns were observed in the studied specimens. Moreover, several carbonates like calcite (CaCO3), ankerite (FeCa(CO3)2) and dolomite (CaMg(CO3)2) were identified only in the lichen thallus vicinity. These evidences are described by means of Raman spectroscopy for the first time. Copyright © 2016 John Wiley & Sons, Ltd.