This work concerns the study of colors and dyes identified on archaeological textiles from the Atacama Desert. The different garments and ornaments come from the excavation of two important pre-Columbian cemeteries of the Tarapacá region: Tarapacá-40 attributed to the Formative period (1100 BC–660 AD) and Pica-8 to the Late Intermediate period (900–1450 AD). For the first time, a multi-analytical approach with non-invasive techniques using FORS and SERS was applied on samples of less than 2 cm of length for physicochemical characterization of the raw materials and the dyes employed in the textile production of northern Chile. The fibers are from animal origin. Blue, green, and yellow are identified as indigo, but we cannot discard a mixture with other dyes to vary hue and shade; while carminic acid and alizarin—to a lesser extent—are found on red, orange, and brown samples. This research provides new elements for the discussion about the textile technology developed in this desertic region, its changes, and continuities along the history. Our results are compared to recent findings on neighboring regions from South-Central Andes, to improve the current knowledge and discuss the existence of dyeing textile cultural traditions.