© 2020 by the authors. The inflorescences of Chamaedorea tepejilote Liebm. are consumed as food in Central America and southern Mexico but is an underutilized food because of its sensory characteristics, principally due to its bitter taste. However, the inflorescences of Chamaedorea tepejilote Liebm. are nutritionally promising due to their high protein content (approximately 25%). Protein isolates from pacaya were modified via three different thermal treatments to determine the effect of the treatments on the protein structures. Scanning electron microscopy indicated that the pacaya protein isolate particles had less rough and irregular surfaces with larger particle sizes due to an aggregation process when a thermal treatment was used compared to those when no thermal treatment was used. An increase in the intensity of the low molecular weight protein fractions (≤20 kDa) in the electrophoretic pattern of the proteins was observed, which was generated by the hydrolysis of the proteins by heat treatment. The modifications in the FT-IR spectra showed that thermal treatment of pacaya affected the secondary structure of its proteins, mainly when microwave treatment was used. Raman spectroscopy revealed that the α-helical structure was dominant in the proteins of pacaya and that thermal treatment increased the fraction of the β-sheet structure at the expense of the α-helical structure.