Micro-Raman spectroscopy was used to analyze and identify pigments and determine the palette of color in wall paintings from four churches of the Colonial Period, in the Bolivian highlands. The ancient churches Santiago de Callapa, Curahuara de Carangas, NuestraSeñora de Copacabana de Andamarca and San José de Soracachi were constructed during the 17th and 18th centuries, around the important colonial Ruta de la Plata, between Potosí city and Arica harbor on the Pacific coast of South America. Most pigments used in the wall paintings correspond to inorganic minerals as well as to organic colorants. Fully chlorinated copper phthalocyanine (green), copper phthalocyanine (blue), β-naphthol (yellow) and benzoimidazolone (red), were identified in the corresponding colored areas suggesting subsequent recent interventions or restorations. Ground layer materials were also characterized. The present results allow for discussion of the pictorial techniques used in the Andean highland during the colonial period and allow conservators and restorers to make important decisions regarding the type of intervention to perform in the case of these important historical and patrimonial monuments.