This article presents the early ATR-FTIR and FORS results of the analysis carried out in five polychrome wooden ceilings from different Jesuit Spanish colonial mission churches. These mission churches date between 1674 and 1723 and are located in the rural villages of Santa Maria, Cusihuiriachi, Coyachi, La Joya, and Rosario in the Northern Mexican State of Chihuahua. The decorative motifs in all five church sites were executed using a similar color palette and painting technique although the pictorial quality differs from one site to the next. The samples collected from the interior of the La Asuncion de Santa Maria de Cuevas are of considerable importance as this site is one of the most significant models of colonial architecture, containing some of the oldest examples of colonial figurative art in Northern Mexico. The scope of this research is to identify and compare the pigments and techniques used in the decorative surfaces of these five selected mission churches. Preliminary FTIR results have unexpectedly determined the presence of indigo and cochineal (not traditionally used among Chihuahua natives) and possibly a mixture of both to produce different tones to decorate the wooden ceilings and choirs of the five missions studied. (c) 2016 Wiley Periodicals, Inc. Col Res Appl, 41, 289-293, 2016