Taking advantage of the recent development of Raman microprobe (RMP) and infrared reflection spectroscopy (IRS) techniques, we report for the first time the mineralogical composition of pre-Columbian Mesoamerican ceramic materials from two sites: Cuanalan (Teotihuacán, Mexico) and Kaminaljuyú area (Guatemala). The Raman spectra obtained from selected areas of the rough fragments from the Cuanalan ceramic materials show that these samples are characterized by the highly heterogeneous body matrix mineralogy due to the presence of a large variety of minerals such as alkali and plagioclase feldspars, diopside, magnetite and Ti-magnetite, and rutile. This mineralogical assemblage including a confirmed diopside is characteristic for the clays that start to crystallize at a temperature near to 800–900 °C. Representative FTIR reflection spectra of the ceramic matrix of Cuanalan pottery in the 1700–400 cm−1 were indicative of non-calcareous ceramic materials, showing strong SiO vibration of meta-clay. The RMP studies of the Mayan ceramics from Guatemala have shown their different mineralogy and chemistry. Due to the presence of calcite (characteristic Raman CO2−3 lines at 1089, 714 and 285 cm−1 were observed) and the absence of diopside and rutile in ceramic pottery from the Kaminaljuyú area, a firing temperature between 600 and 700 °C can be deduced. The IRS spectra indicate a weakly calcareous ceramic matrix with CO32− vibration of microcrystalline calcite. The main CO2−3 reflection bands (at 1530, 1442, 880, and 726 cm−1) were obtained in the heterogeneous samples by using an infrared microscope capable of distinguishing small mineral inclusions and eliminating the characteristic bands of the silicate matrix in the range 1047–1055 cm−1. The detection of anatase polymorph in the Kaminaljuyú pottery demonstrates the content of kaolinite in the raw material. The combined application of RMP and IRS improves the identification of the mineral phases in the composition of the pottery and makes it possible to analyze the structural degree of ordering of the principal amorphous phases that are formed during the firing of the clayey raw material to pottery. With the recent development of combined RMP and IRS techniques, these spectroscopic methods are emerging as an important tools in mineralogical research and, in particular, in the case of in situ studies of archaeological artifacts.