This work describes the characterization of green pigments in wall paintings from the Andean churches of San José de Soracachi and Santiago de Callapa in Bolivia, located on an ancient colonial commercial route known as the Silver Route. To approach our goal, microsamples extracted from the mural paintings and mineral samples, from a mine of the same area, were studied by using micro-Raman spectroscopy complemented with micro-energy-dispersive X-ray fluorescence spectroscopy (μ-EDXRF) and scanning electron microscopy with energy-dispersive X-ray spectroscopy (SEM-EDS) analysis. The use of gypsum as the preparation layer was detected, and it suggests a secco painting technique. Antlerite, a basic copper sulfate, was identified suggesting a preference for its use as green pigment in the mural paintings of Andean churches that may be related to the local availability of this mineral. Indeed, this study revealed the presence of heterogeneous particles of the basic copper sulfate together with aluminosilicates, quartz and iron oxides among others, which points to a mineral origin of the green pigment because the same compounds were found in the samples taken in the mine. Because a phase transition has been noticed during the Raman analyses, due to a high power of the laser radiation, some tests have been carried out, varying the laser power, and coupling the Raman spectrometer to a temperature-controlled stage to verify under which conditions the degradation of the mineral sample of antlerite occurs