The colours used in Pre-Hispanic Mesoamerica to decorate walls, codices or artefacts have been the subject of numerous studies, with particular attention to Maya blue, red and white pigments. However, most of these studies have been focused on emblematic cultures of the Classic period (ca. 300–1000 CE), such as Teotihuacan and Maya cultures. This work proposes a new chronology of the preparation and use of these pigments, particularly Maya blue, by analysing samples of the Pre-Classic period (ca. 1800 BCE–300 CE). The samples belong to ceremonial artefacts decorated with blue, red and white pigments, in a funerary context from the Chupicuaro culture, which was developed between 600 and 100 BCE in Western Mexico. The analytical results obtained in this research by spectroscopic and chromatographic techniques (EDXRF, SEM-EDX, Raman and LC-MS/MS-TOF/MS) confirm the presence of indigo (Indigofera suffruticosa L., Indigofera mucrolata or Indigofera jamaicensis, among other local species), iron oxide (α-Fe2O3), cinnabar (HgS) and calcium carbonate (CaCO3) as compounds of these colours. Our findings support the first evidence of the use of the indigo to elaborate a Maya blue pigment outside the Maya region at least four centuries before it was recognized in this region. Moreover, we found an ancient use of cinnabar mixed together with iron-based red pigments to cover bodies in the burial rites in Pre-Columbian societies, showing a connection between these red pigments and the funerary world in ancient America. These results have a great impact on the history of colour in ancient Mesoamerica from the economic, social, cultural and historical point of view. This study implies a geographical and chronological leap of high impact on the archaeology and history of ancient Mesoamerica.