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In this data article, we present the spectroscopic structural data of the pottery samples collected from Petén Itzá, Guatemala. Detailed Fourier transmission infrared, powder X-ray diffraction, scanning electron microscopy coupled to electron dispersive X-ray diffraction, and thermal gravimetric analysis/differential thermal gravimetric analysis (FTIR, PXRD, SEM/EDX, and TGA/DTGA) were discussed in the research article titled “Comprehensive Structural and Compositional Investigation of Maya Pottery Sherds from Lake Petén Itzá, Guatemala, Central America” (Onchoke et al. 2020 [1]). The FTIR, XRD profiles and composition of pottery from Petén Itzá, Guatemala are presented. This data is important and useful for further understanding of the structural composition of pottery sherds used by Maya people of Guatemala. In addition, the TGA/DTGA profiles provide information on the content of the losses upon heating and offers supportive evidence to the spectroscopic data studied.