In this work, scanning electron microscopy (SEM), X-ray diffraction (XRD), and infrared spectroscopy (FTIR) techniques were used to study blue, red, and ochre pigments from wall paintings of the 16th century colonial convent of San Nicolás de Tolentino in Actopan, Hidalgo, Mexico. In the blue pigments, nanometric fibers with a chemical composition of mostly O, Si, Al, and Mg were identified. XRD and FTIR analysis indicated the presence of palygorskite clay, which suggests that these analyzed blue pigments are similar to Mayan blue. In the red pigment, structures with different morphologies (spines and flake shapes, for instance), with a composition of C, O, Al, Si, S, Ca, Na, Mg, and K and a higher concentration of Fe and Pb, were observed. Complementary analysis showed that the red color originates from hematite and lead. Finally, the ochre pigment showed a significant presence of O and Fe, which was associated with the goethite mineral, while calcite was a crystalline phase identified in all analyzed pigments; these show that these pigments are characteristic of the known Mexican Colonial color palette.